I also commited a much larger swath of hiseq summary files.
One change is Summary and LaneResultSummary now has subclasses to
handle the differences between the GA series and the HiSeq series
runfolders.
At this point the test code is dying trying to read the LaneParameters
out of the gerald config file.
if os.stat(self.pathname)[stat.ST_SIZE] == 0:
raise RuntimeError("Eland isn't done, try again later.")
- LOGGER.info("summarizing results for %s" % (self.pathname))
+ LOGGER.debug("summarizing results for %s" % (self.pathname))
stream = autoopen(self.pathname, 'r')
if self.eland_type == ELAND_SINGLE:
full_lane_id = "%d_%d" % ( lane_id, end )
basename = pattern % (full_lane_id,)
- LOGGER.info("Eland pattern: %s" %(basename,))
+ LOGGER.debug("Eland pattern: %s" %(basename,))
pathname = os.path.join(basedir, basename)
if os.path.exists(pathname):
LOGGER.info('found eland file in %s' % (pathname,))
import stat
import time
-from htsworkflow.pipelines.summary import Summary
+from htsworkflow.pipelines.summary import Summary, SummaryGA, SummaryHiSeq
from htsworkflow.pipelines.eland import eland, ELAND
from htsworkflow.pipelines.runfolder import \
# parse Summary.htm file
summary_xml = os.path.join(g.pathname, 'Summary.xml')
summary_htm = os.path.join(g.pathname, 'Summary.htm')
- status_files_summary = os.path.join(g.pathname, '..', 'Data', 'Status_Files', 'Summary.htm')
+ report_summary = os.path.join(g.pathname, '..', 'Data',
+ 'reports', 'Summary', )
if os.path.exists(summary_xml):
LOGGER.info("Parsing Summary.xml")
- summary_pathname = summary_xml
+ g.summary = SummaryGA(summary_xml)
+ g.eland_results = eland(g.pathname, g)
elif os.path.exists(summary_htm):
- summary_pathname = os.path.join(g.pathname, 'Summary.htm')
LOGGER.info("Parsing Summary.htm")
- else:
- summary_pathname = status_files_summary
- LOGGER.info("Parsing %s" % (status_files_summary,))
- g.summary = Summary(summary_pathname)
+ g.summary = SummaryGA(summary_htm)
+ g.eland_results = eland(g.pathname, g)
+ elif os.path.isdir(report_summary):
+ LOGGER.info("Parsing %s" % (report_summary,))
+ g.summary = SummaryHiSeq(report_summary)
+
# parse eland files
- g.eland_results = eland(g.pathname, g)
return g
if __name__ == "__main__":
"""
Analyze the Summary.htm file produced by GERALD
"""
+import os
import logging
import re
import types
XML_VERSION = 3
SUMMARY = 'Summary'
- class LaneResultSummary(object):
- """
- Parse the LaneResultSummary table out of Summary.htm
- Mostly for the cluster number
- """
- LANE_RESULT_SUMMARY = 'LaneResultSummary'
- TAGS = {
- 'LaneYield': 'lane_yield',
- 'Cluster': 'cluster', # Raw
- 'ClusterPF': 'cluster_pass_filter',
- 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
- 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
- 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
- 'PercentPassFilterAlign': 'percent_pass_filter_align',
- 'AverageAlignmentScore': 'average_alignment_score',
- 'PercentErrorRate': 'percent_error_rate'
- }
- # These are tags that have mean/stdev as found in the GERALD Summary.xml file
- GERALD_TAGS = {
- #'laneYield': 'lane_yield', #this is just a number
- 'clusterCountRaw': 'cluster', # Raw
- 'clusterCountPF': 'cluster_pass_filter',
- 'oneSig': 'average_first_cycle_intensity',
- 'signal20AsPctOf1': 'percent_intensity_after_20_cycles',
- 'percentClustersPF': 'percent_pass_filter_clusters',
- 'percentUniquelyAlignedPF': 'percent_pass_filter_align',
- 'averageAlignScorePF': 'average_alignment_score',
- 'errorPF': 'percent_error_rate'
- }
-
- def __init__(self, html=None, xml=None):
- self.lane = None
- self.end = 0
- self.lane_yield = None
- self.cluster = None
- self.cluster_pass_filter = None
- self.average_first_cycle_intensity = None
- self.percent_intensity_after_20_cycles = None
- self.percent_pass_filter_clusters = None
- self.percent_pass_filter_align = None
- self.average_alignment_score = None
- self.percent_error_rate = None
-
- if html is not None:
- self.set_elements_from_source(html)
- if xml is not None:
- self.set_elements(xml)
-
- def set_elements_from_source(self, data):
- """Read from an initial summary data file. Either xml or html
- """
- if not len(data) in (8,10):
- raise RuntimeError("Summary.htm file format changed, len(data)=%d" % (len(data),))
-
- # same in pre-0.3.0 Summary file and 0.3 summary file
- self.lane = int(data[0])
-
- if len(data) == 8:
- parsed_data = [ parse_mean_range(x) for x in data[1:] ]
- # this is the < 0.3 Pipeline version
- self.cluster = parsed_data[0]
- self.average_first_cycle_intensity = parsed_data[1]
- self.percent_intensity_after_20_cycles = parsed_data[2]
- self.percent_pass_filter_clusters = parsed_data[3]
- self.percent_pass_filter_align = parsed_data[4]
- self.average_alignment_score = parsed_data[5]
- self.percent_error_rate = parsed_data[6]
- elif len(data) == 10:
- parsed_data = [ parse_mean_range(x) for x in data[2:] ]
- # this is the >= 0.3 summary file
- self.lane_yield = data[1]
- self.cluster = parsed_data[0]
- self.cluster_pass_filter = parsed_data[1]
- self.average_first_cycle_intensity = parsed_data[2]
- self.percent_intensity_after_20_cycles = parsed_data[3]
- self.percent_pass_filter_clusters = parsed_data[4]
- self.percent_pass_filter_align = parsed_data[5]
- self.average_alignment_score = parsed_data[6]
- self.percent_error_rate = parsed_data[7]
-
- def set_elements_from_gerald_xml(self, read, element):
- self.lane = int(element.find('laneNumber').text)
- self.end = read
- lane_yield_node = element.find('laneYield')
- if lane_yield_node is not None:
- self.lane_yield = int(lane_yield_node.text)
- else:
- self.lane_yield = None
-
- for GeraldName, LRSName in Summary.LaneResultSummary.GERALD_TAGS.items():
- node = element.find(GeraldName)
- if node is None:
- LOGGER.info("Couldn't find %s" % (GeraldName))
- setattr(self, LRSName, parse_xml_mean_range(node))
-
- def get_elements(self):
- lane_result = etree.Element(
- Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
- {'lane': unicode(self.lane), 'end': unicode(self.end)})
- for tag, variable_name in Summary.LaneResultSummary.TAGS.items():
- value = getattr(self, variable_name)
- if value is None:
- continue
- # it looks like a sequence
- elif type(value) in (types.TupleType, types.ListType):
- element = make_mean_range_element(
- lane_result,
- tag,
- *value
- )
- else:
- element = etree.SubElement(lane_result, tag)
- element.text = unicode(value)
- return lane_result
-
- def set_elements(self, tree):
- if tree.tag != Summary.LaneResultSummary.LANE_RESULT_SUMMARY:
- raise ValueError('Expected %s' % (
- Summary.LaneResultSummary.LANE_RESULT_SUMMARY))
- self.lane = int(tree.attrib['lane'])
- # default to the first end, for the older summary files
- # that are single ended
- self.end = int(tree.attrib.get('end', 0))
- tags = Summary.LaneResultSummary.TAGS
- for element in list(tree):
- try:
- variable_name = tags[element.tag]
- setattr(self, variable_name,
- parse_summary_element(element))
- except KeyError, e:
- LOGGER.warn('Unrecognized tag %s' % (element.tag,))
-
def __init__(self, filename=None, xml=None):
# lane results is a list of 1 or 2 ends containing
# a dictionary of all the lanes reported in this
def __len__(self):
return len(self.lane_results)
+ def get_elements(self):
+ summary = etree.Element(Summary.SUMMARY,
+ {'version': unicode(Summary.XML_VERSION)})
+ for end in self.lane_results:
+ for lane in end.values():
+ summary.append(lane.get_elements())
+ return summary
+
+ def set_elements(self, tree):
+ if tree.tag != Summary.SUMMARY:
+ return ValueError("Expected %s" % (Summary.SUMMARY,))
+ xml_version = int(tree.attrib.get('version', 0))
+ if xml_version > Summary.XML_VERSION:
+ LOGGER.warn('Summary XML tree is a higher version than this class')
+ for element in list(tree):
+ lrs = LaneResultSummaryGA()
+ lrs.set_elements(element)
+ if len(self.lane_results) < (lrs.end + 1):
+ self.lane_results.append({})
+ self.lane_results[lrs.end][lrs.lane] = lrs
+
+ def is_paired_end(self):
+ return len(self.lane_results) == 2
+
+ def dump(self):
+ """
+ Debugging function, report current object
+ """
+ tree = self.get_elements()
+ print etree.tostring(tree)
+
+class SummaryGA(Summary):
+ def __init__(self, filename=None, xml=None):
+ super(SummaryGA, self).__init__(filename, xml)
+
def _flattened_row(self, row):
"""
flatten the children of a <tr>...</tr>
read = int(read_tree.find('readNumber').text)-1
for element in read_tree.getchildren():
if element.tag.lower() == "lane":
- lrs = Summary.LaneResultSummary()
+ lrs = LaneResultSummaryGA()
lrs.set_elements_from_gerald_xml(read, element)
self.lane_results[lrs.end][lrs.lane] = lrs
# probably not useful
self.lane_results.append({})
for r in lane_summary:
- lrs = Summary.LaneResultSummary(html=r)
+ lrs = LaneResultSummaryGA(html=r)
lrs.end = end
self.lane_results[lrs.end][lrs.lane] = lrs
###### END HTML Table Extraction ########
+
+class SummaryHiSeq(Summary):
+ def __init__(self, filename=None, xml=None):
+ super(SummaryHiSeq, self).__init__(filename, xml)
+
+ def _extract_lane_results(self, filename):
+ read1 = os.path.join(filename, 'read1.xml')
+ read2 = os.path.join(filename, 'read2.xml')
+
+ if os.path.exists(read1):
+ self._extract_lane_results_for_end(read1, 0)
+ else:
+ LOGGER.warn("No read1.xml at %s." % (read1,))
+ if os.path.exists(read2):
+ self.lane_results.append({})
+ self._extract_lane_results_for_end(read2, 1)
+
+ def _extract_lane_results_for_end(self, filename, end):
+ self.tree = etree.parse(filename)
+ root = self.tree.getroot()
+ for lane in root.getchildren():
+ lrs = LaneResultSummaryHiSeq(data=lane)
+ lrs.end = end
+ self.lane_results[lrs.end][lrs.lane] = lrs
+
+
+class LaneResultSummary(object):
+ """
+ Parse the LaneResultSummary table out of Summary.htm
+ Mostly for the cluster number
+ """
+ LANE_RESULT_SUMMARY = 'LaneResultSummary'
+ TAGS = {
+ 'LaneYield': 'lane_yield',
+ 'Cluster': 'cluster', # Raw
+ 'ClusterPF': 'cluster_pass_filter',
+ 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
+ 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
+ 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
+ 'PercentPassFilterAlign': 'percent_pass_filter_align',
+ 'AverageAlignmentScore': 'average_alignment_score',
+ 'PercentErrorRate': 'percent_error_rate'
+ }
+ # These are tags that have mean/stdev as found in the GERALD Summary.xml file
+ GERALD_TAGS = {
+ #'laneYield': 'lane_yield', #this is just a number
+ 'clusterCountRaw': 'cluster', # Raw
+ 'clusterCountPF': 'cluster_pass_filter',
+ 'oneSig': 'average_first_cycle_intensity',
+ 'signal20AsPctOf1': 'percent_intensity_after_20_cycles',
+ 'percentClustersPF': 'percent_pass_filter_clusters',
+ 'percentUniquelyAlignedPF': 'percent_pass_filter_align',
+ 'averageAlignScorePF': 'average_alignment_score',
+ 'errorPF': 'percent_error_rate'
+ }
+
+ def __init__(self, html=None, xml=None):
+ self.lane = None
+ self.end = 0
+ self.lane_yield = None
+ self.cluster = None
+ self.cluster_pass_filter = None
+ self.average_first_cycle_intensity = None
+ self.percent_intensity_after_20_cycles = None
+ self.percent_pass_filter_clusters = None
+ self.percent_pass_filter_align = None
+ self.average_alignment_score = None
+ self.percent_error_rate = None
+
+
def get_elements(self):
- summary = etree.Element(Summary.SUMMARY,
- {'version': unicode(Summary.XML_VERSION)})
- for end in self.lane_results:
- for lane in end.values():
- summary.append(lane.get_elements())
- return summary
+ lane_result = etree.Element(
+ LaneResultSummary.LANE_RESULT_SUMMARY,
+ {'lane': unicode(self.lane), 'end': unicode(self.end)})
+ for tag, variable_name in LaneResultSummary.TAGS.items():
+ value = getattr(self, variable_name)
+ if value is None:
+ continue
+ # it looks like a sequence
+ elif type(value) in (types.TupleType, types.ListType):
+ element = make_mean_range_element(
+ lane_result,
+ tag,
+ *value
+ )
+ else:
+ element = etree.SubElement(lane_result, tag)
+ element.text = unicode(value)
+ return lane_result
def set_elements(self, tree):
- if tree.tag != Summary.SUMMARY:
- return ValueError("Expected %s" % (Summary.SUMMARY,))
- xml_version = int(tree.attrib.get('version', 0))
- if xml_version > Summary.XML_VERSION:
- LOGGER.warn('Summary XML tree is a higher version than this class')
+ if tree.tag != LaneResultSummary.LANE_RESULT_SUMMARY:
+ raise ValueError('Expected %s' % (
+ LaneResultSummary.LANE_RESULT_SUMMARY))
+ self.lane = int(tree.attrib['lane'])
+ # default to the first end, for the older summary files
+ # that are single ended
+ self.end = int(tree.attrib.get('end', 0))
+ tags = LaneResultSummary.TAGS
for element in list(tree):
- lrs = Summary.LaneResultSummary()
- lrs.set_elements(element)
- if len(self.lane_results) < (lrs.end + 1):
- self.lane_results.append({})
- self.lane_results[lrs.end][lrs.lane] = lrs
+ try:
+ variable_name = tags[element.tag]
+ setattr(self, variable_name,
+ parse_summary_element(element))
+ except KeyError, e:
+ LOGGER.warn('Unrecognized tag %s' % (element.tag,))
- def is_paired_end(self):
- return len(self.lane_results) == 2
- def dump(self):
+class LaneResultSummaryGA(LaneResultSummary):
+ def __init__(self, html=None, xml=None):
+ super(LaneResultSummaryGA, self).__init__(html, xml)
+
+ if html is not None:
+ self.set_elements_from_source(html)
+ if xml is not None:
+ self.set_elements(xml)
+
+ def set_elements_from_gerald_xml(self, read, element):
+ self.lane = int(element.find('laneNumber').text)
+ self.end = read
+ lane_yield_node = element.find('laneYield')
+ if lane_yield_node is not None:
+ self.lane_yield = int(lane_yield_node.text)
+ else:
+ self.lane_yield = None
+
+ for GeraldName, LRSName in LaneResultSummary.GERALD_TAGS.items():
+ node = element.find(GeraldName)
+ if node is None:
+ LOGGER.info("Couldn't find %s" % (GeraldName))
+ setattr(self, LRSName, parse_xml_mean_range(node))
+
+ def set_elements_from_source(self, data):
+ """Read from an initial summary data file. Either xml or html
"""
- Debugging function, report current object
+ if not len(data) in (8,10):
+ raise RuntimeError("Summary.htm file format changed, len(data)=%d" % (len(data),))
+
+ # same in pre-0.3.0 Summary file and 0.3 summary file
+ self.lane = int(data[0])
+
+ if len(data) == 8:
+ parsed_data = [ parse_mean_range(x) for x in data[1:] ]
+ # this is the < 0.3 Pipeline version
+ self.cluster = parsed_data[0]
+ self.average_first_cycle_intensity = parsed_data[1]
+ self.percent_intensity_after_20_cycles = parsed_data[2]
+ self.percent_pass_filter_clusters = parsed_data[3]
+ self.percent_pass_filter_align = parsed_data[4]
+ self.average_alignment_score = parsed_data[5]
+ self.percent_error_rate = parsed_data[6]
+ elif len(data) == 10:
+ parsed_data = [ parse_mean_range(x) for x in data[2:] ]
+ # this is the >= 0.3 summary file
+ self.lane_yield = data[1]
+ self.cluster = parsed_data[0]
+ self.cluster_pass_filter = parsed_data[1]
+ self.average_first_cycle_intensity = parsed_data[2]
+ self.percent_intensity_after_20_cycles = parsed_data[3]
+ self.percent_pass_filter_clusters = parsed_data[4]
+ self.percent_pass_filter_align = parsed_data[5]
+ self.average_alignment_score = parsed_data[6]
+ self.percent_error_rate = parsed_data[7]
+
+
+class LaneResultSummaryHiSeq(LaneResultSummary):
+ def __init__(self, data=None, xml=None):
+ super(LaneResultSummaryHiSeq, self).__init__(data, xml)
+
+ if data is not None:
+ self.set_elements_from_source(data)
+ if xml is not None:
+ self.set_elements(xml)
+
+ def set_elements_from_source(self, element):
+ """Read from an initial summary data file. Either xml or html
"""
- tree = self.get_elements()
- print etree.tostring(tree)
+ # same in pre-0.3.0 Summary file and 0.3 summary file
+ lane = element.attrib
+ self.lane = int(lane['key'])
+ #self.lane_yield = data[1]
+ self.cluster = (int(lane['ClustersRaw']),
+ float(lane['ClustersRawSD']))
+ self.cluster_pass_filter = (int(lane['ClustersPF']),
+ float(lane['ClustersPFSD']))
+ self.average_first_cycle_intensity = (int(lane['FirstCycleIntPF']),
+ float(lane['FirstCycleIntPFSD']))
+ self.percent_intensity_after_20_cycles = (
+ float(lane['PrcIntensityAfter20CyclesPF']),
+ float(lane['PrcIntensityAfter20CyclesPFSD']))
+ self.percent_pass_filter_clusters = (
+ float(lane['PrcPFClusters']),
+ float(lane['PrcPFClustersSD']))
+ self.percent_pass_filter_align = (
+ float(lane['PrcAlign']),
+ float(lane['PrcAlignSD']))
+ self.percent_error_rate = (
+ float(lane['ErrRatePhiX']),
+ float(lane['ErrRatePhiXSD']),)
+
def tonumber(v):
"""
def make_aligned_config_1_12(aligned_dir):
"""This is rouglhly equivalent to the old gerald file"""
- source = os.path.join(TESTDATA_DIR, 'aligned_config_1_12.xml')
+ source = os.path.join(TESTDATA_DIR, '1_12', 'aligned_config_1_12.xml')
destination = os.path.join(aligned_dir, 'config.xml')
shutil.copy(source, destination)
def make_unaligned_config_1_12(unaligned_dir):
demultiplex_pairs = [ # (src,
# dest),
- (os.path.join(TESTDATA_DIR, 'demultiplex_1.12.4.2.xml'),
+ (os.path.join(TESTDATA_DIR, '1_12', 'demultiplex_1.12.4.2.xml'),
os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
- (os.path.join(TESTDATA_DIR, 'demultiplexed_bustard_1.12.4.2.xml'),
+ (os.path.join(TESTDATA_DIR, '1_12',
+ 'demultiplexed_bustard_1.12.4.2.xml'),
os.path.join(unaligned_dir, 'DemultiplexedBustardConfig.xml')),
- (os.path.join(TESTDATA_DIR, 'demultiplexed_summary_1.12.4.2.xml'),
+ (os.path.join(TESTDATA_DIR, '1_12',
+ 'demultiplexed_summary_1.12.4.2.xml'),
os.path.join(unaligned_dir, 'DemultiplexedBustardSummary.xml')),
]
for src, dest in demultiplex_pairs:
if not os.path.exists(intensities_dir):
os.mkdir(intensities_dir)
- param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.12.4.2.xml')
+ param_file = os.path.join(TESTDATA_DIR, '1_12',
+ 'rta_intensities_config_1.12.4.2.xml')
shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
return intensities_dir
os.mkdir(basecalls_dir)
make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
- param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.12.4.2.xml')
+ param_file = os.path.join(TESTDATA_DIR, '1_12',
+ 'rta_basecalls_config_1.12.4.2.xml')
shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
return basecalls_dir
destination = os.path.join(gerald_dir, 'Summary.xml')
shutil.copy(source, destination)
-def make_summary_rta1_12(status_dir):
- source = os.path.join(TESTDATA_DIR, 'Summary-rta1_12.htm')
- destination = os.path.join(status_dir, 'Summary.htm')
- shutil.copy(source, destination)
+def make_status_rta1_12(datadir):
+ sourcedir = os.path.join(TESTDATA_DIR, '1_12')
+ status_htm = os.path.join(sourcedir, 'Status.htm')
+ destination = os.path.join(datadir, 'Status.htm')
+ shutil.copy(status_htm, destination)
+
+ status_dir = os.path.join(datadir, 'Status_Files')
+ status_source_dir = os.path.join(sourcedir, 'Status_Files')
+ shutil.copytree(status_source_dir, status_dir)
+
+ report_source_dir = os.path.join(sourcedir, 'reports')
+ report_dir = os.path.join(datadir, 'reports')
+ shutil.copytree(report_source_dir, report_dir)
def make_eland_results(gerald_dir):
eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
os.mkdir(data_dir)
intensities_dir = make_rta_intensities_1_12(data_dir)
-
- status_dir = os.path.join(data_dir, 'Status_Files')
- os.mkdir(status_dir)
- make_summary_rta1_12(status_dir)
+ make_status_rta1_12(data_dir)
basecalls_dir = make_rta_basecalls_1_12(intensities_dir)
make_matrix_dir_rta_1_12(basecalls_dir)
def test_xml_summary_file(self):
pathname = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
- s = summary.Summary(pathname)
+ s = summary.SummaryGA(pathname)
self.failUnlessEqual(len(s.lane_results[0]), 8)
self.failUnlessEqual(s.lane_results[0][1].cluster, (1073893, 146344))
def test_html_summary_file(self):
pathname = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
- s = summary.Summary(pathname)
+ s = summary.SummaryGA(pathname)
self.failUnlessEqual(len(s.lane_results[0]), 8)
self.failUnlessEqual(s.lane_results[0][1].cluster, (126910, 4300))
def test_hiseq_sample_summary_file(self):
pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
- s = summary.Summary(pathname)
+ s = summary.SummaryGA(pathname)
def suite():
return unittest.makeSuite(SummaryTests,'test')
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status_Files/Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status_Files/Status.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+<body>\r
+<table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./Status_Files/RefreshBtn/r1.png" onmouseout="this.src='./Status_Files/RefreshBtn/r1.png'" onmouseover="this.src='./Status_Files/RefreshBtn/r2.png'" onmousedown="this.src='./Status_Files/RefreshBtn/r3.png'" onmouseup="this.src='./Status_Files/RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('./reports/StatusUpdate.xml', './Status_Files/StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('./reports/Status.xml'), loadXMLDoc('./Status_Files/RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+</script>\r
+<ul id="tabmenu">\r
+ <li><a href="./Status_Files/RunInfo.htm">Run Info</a></li>\r
+ <li><a class="selected" href="Status.htm">Tile Status</a></li>\r
+ <li><a href="./Status_Files/Charts.htm">Charts</a></li>\r
+ <li><a href="./Status_Files/Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./Status_Files/ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./Status_Files/ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+<div id="container">\r
+ <img class="Chart" id="ProcessControlImg" src="./reports/Process Control.png" alt="Cannot display image"/>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./ByCycle.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ var runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+\r
+<ul id="tabmenu">\r
+\r
+\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a class="selected" href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <form action="" name="Plot1" id="Plot1" style="margin: 0px 0px 0px 0px;">\r
+ <table style="border:none"><tr>\r
+ <td><img style="margin: 0px 0px -5px 0px;" alt="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="changeFrameSrc(Plot1)" /> </td>\r
+ <td><select size="1" name="QCOptDropDown" onchange="changeFrameSrc(this.form)">\r
+ <option value="Intensity" selected="selected">Intensity</option>\r
+ <option value="FWHM">Focus Quality</option>\r
+ <option value="QScore">Quality Score</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrRate">Error Rate</option>\r
+ </select>  </td> \r
+ <td><select size="1" name="lanesDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="L0" selected="selected">All Lanes</option>\r
+ <option value="L1">Lane 1</option>\r
+ <option value="L2">Lane 2</option>\r
+ <option value="L3">Lane 3</option>\r
+ <option value="L4">Lane 4</option>\r
+ <option value="L5">Lane 5</option>\r
+ <option value="L6">Lane 6</option>\r
+ <option value="L7">Lane 7</option>\r
+ <option value="L8">Lane 8</option>\r
+ </select>  </td>\r
+ <td><select size="1" name="baseDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="A">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select></td>\r
+ </tr></table> \r
+ <iframe name="Plot1Fr" src="./ByCycleFrame.htm?../reports/ByCycle/Intensity_L0a.png" height="387" width="95%" frameborder="0" >\r
+ <img name="imgPlot" alt="No Data" src="../reports/ByCycle/Intensity_L0a.png"/>\r
+ </iframe >\r
+ </form >\r
+ <form action="" name="Plot2" id="Plot2" style="margin: 0px 0px 0px 0px;">\r
+ <table style="border:none"><tr>\r
+ <td><img style="margin: 0px 0px -5px 0px;" alt="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="changeFrameSrc(Plot2)" /> </td>\r
+ <td><select size="1" name="QCOptDropDown" onchange="changeFrameSrc(this.form)">\r
+ <option value="Intensity">Intensity</option>\r
+ <option value="FWHM" selected="selected">Focus Quality</option>\r
+ <option value="QScore">Quality Score</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrRate">Error Rate</option>\r
+ </select>  </td> \r
+ <td><select size="1" name="lanesDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="L0" selected="selected">All Lanes</option>\r
+ <option value="L1">Lane 1</option>\r
+ <option value="L2">Lane 2</option>\r
+ <option value="L3">Lane 3</option>\r
+ <option value="L4">Lane 4</option>\r
+ <option value="L5">Lane 5</option>\r
+ <option value="L6">Lane 6</option>\r
+ <option value="L7">Lane 7</option>\r
+ <option value="L8">Lane 8</option>\r
+ </select>  </td>\r
+ <td><select size="1" name="baseDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="A">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select></td>\r
+ </tr></table> \r
+ <iframe name="Plot2Fr" src="./ByCycleFrame.htm?../reports/ByCycle/FWHM_L0a.png" height="387" width="95%" frameborder="0">\r
+ <img name="imgPlot" alt="No Data" src="../reports/ByCycle/FWHM_L0a.png"/>\r
+ </iframe >\r
+ </form >\r
+</div>\r
+</body>\r
+</html>\r
+\r
--- /dev/null
+\r
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function changeFrameSrc(form) {\r
+ var imgName = null;\r
+ var base = "";\r
+ var qc = form.QCOptDropDown.value;\r
+ if (qc == 'QScore' || qc == 'NumGT30' || qc == 'ErrRate') {\r
+ form.baseDropDown.style.display = 'none';\r
+ } else {\r
+ form.baseDropDown.style.display = 'inline';\r
+ base = form.baseDropDown.value.toLowerCase();\r
+ };\r
+ var intensityURL = "../reports/IntensityFrame.htm?";\r
+\r
+ imgName = "../reports/ByCycle/" + form.QCOptDropDown.value + "_" + form.lanesDropDown.value + base + ".png";\r
+ if (window.frames[form.name + "Fr"] != null) window.frames[form.name + "Fr"].location = "./ByCycleFrame.htm?" + imgName;\r
+ if (form.imgPlot != null) form.imgPlot.src = "../reports/" + imgName;\r
+}\r
+\r
+\r
--- /dev/null
+<html xmlns="http://www.w3.org/1999/xhtml">\r
+<head>\r
+<script type="text/javascript">\r
+ function setupImage() {\r
+ document.PlotImage.src = getParam() + "?" + (new Date().getMilliseconds());\r
+ document.PlotImage.style.display = "block"\r
+ }\r
+ function getParam() {\r
+ return location.href.substring(location.href.indexOf('?') + 1, location.href.length);\r
+ }\r
+</script>\r
+</head>\r
+<body onload='try{setupImage()}catch(err){};'>\r
+ <img name="PlotImage" id="PlotImage" title="Data by cycle" style="display:none" src="#" alt="No data"/>\r
+</body>\r
+</html>\r
+\r
+\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./ByLane.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ var runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a class="selected" href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+\r
+</ul>\r
+ \r
+<div id="container">\r
+ <p style="margin: 0px 0px 0px 120px;">\r
+ <input type="checkbox" name="PFOnlyBox" id="PFOnlyBox" title="Show only PF clusters" onclick="loadClustersByLane()"/>\r
+ Show PF only\r
+ </p>\r
+ <img class="Chart" alt="No Data" id="NumClustersImg" src="../reports/NumClusters By Lane.png"/>\r
+ <table class="DataTable" style="margin: 0px 0px 0px 20px" id="NumClustersTbl"></table >\r
+ <script type="text/javascript">loadClustersByLane();</script>\r
+</div>\r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function loadClustersByLane() {\r
+ name = name0 = '../reports/NumClusters By Lane';\r
+ if (document.getElementById('PFOnlyBox').checked) {\r
+ name = name0 + " PF";\r
+ try {\r
+ xmlDoc = loadXMLDoc(name + '.xml');\r
+ } catch (e) { xmlDoc = null; };\r
+ if (xmlDoc == null || xmlDoc.getElementsByTagName('Data') == null) {\r
+ name = name0;\r
+ alert("No data available!");\r
+ document.getElementById('PFOnlyBox').checked = false;\r
+ }\r
+ }\r
+ document.getElementById('NumClustersImg').src = name + ".png";\r
+ imgRefresh('NumClustersImg');\r
+ loadNumClustersTable(name + '.xml', 'NumClustersTbl', 'Lane');\r
+}\r
+\r
+function loadNumClustersTable(xmlName, tblName, tagsName) {\r
+ tbl = document.getElementById(tblName);\r
+ xmlDoc = loadXMLDoc(xmlName);\r
+ if (xmlDoc == null) return;\r
+ xmlRows = xmlDoc.getElementsByTagName(tagsName);\r
+ if (xmlRows == null) return;\r
+ while (tbl.rows.length > 0) tbl.deleteRow(tbl.rows.length - 1);\r
+ if (xmlRows.length > 0 && xmlRows[0].attributes.length > 0) {\r
+ tbl.insertRow(0);\r
+ for (j = xmlRows[0].attributes.length - 1; j >= 1; j--)\r
+ tbl.insertRow(0);\r
+ for (i = xmlRows.length - 1; i >= 0; i--) {\r
+ for (j = xmlRows[i].attributes.length - 1; j >= 1; j--) {\r
+ tbl.rows[j].insertCell(0);\r
+ val = new Number(xmlRows[i].attributes[j].value);\r
+ if (val < 1000) strVal = val.toFixed(0);\r
+ else strVal = (val / 1000).toFixed(0) + "K";\r
+ tbl.rows[j].cells[0].innerHTML = strVal;\r
+ }\r
+ }\r
+ for (j = xmlRows[0].attributes.length - 1; j >= 1; j--) {\r
+ tbl.rows[j].insertCell(0);\r
+ tbl.rows[j].cells[0].innerHTML = xmlRows[0].attributes[j].name.toUpperCase();\r
+ //tbl.rows[j].insertCell(0); tbl.rows[j].insertCell(0);\r
+ }\r
+ for (i = xmlRows.length - 1; i >= 0; i--) {\r
+ tbl.rows[0].insertCell(0);\r
+ tbl.rows[j].cells[0].innerHTML = tagsName + " " + xmlRows[i].attributes[0].value;\r
+ }\r
+ tbl.rows[0].insertCell(0); //tbl.rows[0].insertCell(0); tbl.rows[0].insertCell(0);\r
+ }\r
+}\r
+\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Charts.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ var runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+ <map name="tileMap" id = "tileMap"></map> \r
+ <script type="text/javascript">\r
+ var tilesPerLane = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./TilesPerLane.xsl'));\r
+ var tileMap = new TileMap(tilesPerLane);\r
+ var imgCycle = document.getElementById("ImgCycle");\r
+ if (imgCycle != null) imgCycle = imgCycle.innerHTML;\r
+ else imgCycle = 0;\r
+ </script>\r
+\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a class="selected" href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <table class="GreenLife" ><tr>\r
+ <td><form name="imgChartForm1" action="">\r
+ <select size="1" name="QCOptDropDown" onchange="changeImage(this.form)">\r
+ <option value="NumClusters" selected="selected">Cluster Density</option>\r
+ <option value="PassedFilter25">%Cluster PF</option>\r
+ <option value="NumPassedFilter25">Cluster PF Density</option>\r
+ </select> \r
+      <label id="autoscale1lbl" for='autoscale1'>Autoscale </label><input type="checkbox" name="autoscale" id="autoscale1" title="Autoscale" onclick="changeImage(this.form)"/>\r
+ <img name="Chart" class="Chart" id="imgChart1" src="../reports/NumClusters_Chart.png" usemap="#tileMap" onmouseover="tileMap.resetMap(this)" onerror="try{{if(this.src.indexOf('blank.png') == -1)showBlank('imgChart1'); /*setTimeout('imgReload(\'imgChart1\')',20000)*/}}catch(err){{errorPrint(err)}}" alt= "No Data"/>\r
+ </form ></td>\r
+ <td><form name="imgChartForm2" action=""> \r
+ <select size="1" name="QCOptDropDown" onchange="changeImage(this.form)">\r
+ <option value="Intensity" selected="selected">Intensity </option>\r
+ <option value="FWHM">Focus Quality</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrorRate">Error Rate</option>\r
+ </select> \r
+ <select size="1" name="cyDropDown" onchange="changeImage(this.form)"></select>\r
+ <script type="text/javascript">\r
+ fillCycles(document.imgChartForm2.cyDropDown, imgCycle);\r
+ </script>\r
+ <select size="1" name="baseDropDown" onchange="changeImage(this.form)">\r
+ <option value="A" selected="selected">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select>\r
+   <label id="autoscale2lbl" for='autoscale2' style ="display :none ">Autoscale </label><input type="checkbox" name="autoscale" id="autoscale2" title="Autoscale" onclick="changeImage(this.form)"/>\r
+ <img name="Chart" class="Chart" id="imgChart2" src="../reports/Intensity/Chart_1_a.png" usemap="#tileMap" onmouseover="tileMap.resetMap(this)" onerror="try{{if(this.src.indexOf('blank.png') == -1)showBlank('imgChart2'); /*setTimeout('imgReload(\'imgChart2\')',20000)*/}}catch(err){{errorPrint(err)}}" alt ="No Data"/>\r
+ </form ></td>\r
+ <td><form name="imgChartForm3" action=""> \r
+ <select size="1" name="QCOptDropDown" onchange="changeImage(this.form)">\r
+ <option value="Intensity">Intensity </option>\r
+ <option value="FWHM" selected="selected">Focus Quality</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrorRate">Error Rate</option>\r
+ </select> \r
+ <select size="1" name="cyDropDown" onchange="changeImage(this.form)"></select>\r
+ <script type="text/javascript">\r
+ fillCycles(document.imgChartForm3.cyDropDown, imgCycle);\r
+ </script>\r
+ <select size="1" name="baseDropDown" onchange="changeImage(this.form)">\r
+ <option value="A" selected="selected">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select>\r
+   <label id="autoscale3lbl" for='autoscale3' style ="display :none">Autoscale</label><input type="checkbox" name="autoscale" id="autoscale3" title="Autoscale" onclick="changeImage(this.form)"/>\r
+ <img name="Chart" class="Chart" id="imgChart3" src="../reports/FWHM/Chart_1_a.png" usemap="#tileMap" onmouseover="tileMap.resetMap(this)" onerror="try{{if(this.src.indexOf('blank.png') == -1)showBlank('imgChart3'); /*setTimeout('imgReload(\'imgChart3\')',20000)*/}}catch(err){{errorPrint(err)}}" alt ="No Data"/>\r
+ </form></td>\r
+ </tr></table>\r
+</div> \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+var imageOnFocusId = null;\r
+function TileMap(nTiles) {\r
+ var numLanes = 8;\r
+ var numTiles = nTiles;\r
+ var width = 200;\r
+ var height = 750;\r
+ var X0 = 18;\r
+ var Y0 = 26;\r
+ var dL = width / numLanes;\r
+ var numCols = 2;\r
+ var numRows = numTiles / numCols;\r
+ var dX = width / (numCols * numLanes);\r
+ var dY = height / numRows;\r
+ var map = document.getElementById("tileMap");\r
+ var tileMapXML;\r
+ this.changeLayout = function(layoutNode) {\r
+ nCols = layoutNode.getAttribute("ColsPerLane");\r
+ if (nCols > 0) numCols = nCols;\r
+ nRows = layoutNode.getAttribute("RowsPerLane");\r
+ if (nRows > 0) numRows = nRows;\r
+ dX = width / (numCols * numLanes);\r
+ dY = height / numRows;\r
+ }\r
+ this.newToolTip = function(lane, idx) {\r
+ var area = document.createElement("area");\r
+ area.shape = "rect";\r
+ var col = Math.floor((idx - 1) / numRows);\r
+ var row = (idx - 1) % numRows;\r
+ if (idx - numRows <= 0) row = numRows - row - 1;\r
+ var X1 = Math.round(X0 + dX * col + (lane - 1) * dL);\r
+ var Y1 = Math.round(Y0 + dY * row);\r
+ var X2 = Math.round(X1 + dX);\r
+ var Y2 = Math.round(Y1 + dY);\r
+ area.coords = "'" + X1 + "," + Y1 + "," + X2 + "," + Y2 + "'";\r
+ area.title = "L:" + lane + " T:" + idx;\r
+ map.appendChild(area);\r
+ }\r
+\r
+ this.newToolTipVal = function(tile, base) {\r
+ var area = document.createElement("area");\r
+ area.shape = "rect";\r
+ key = tile.getAttribute("Key");\r
+ if (base == null) base = "Val";\r
+ val = tile.getAttribute(base);\r
+ lane = key.substring(0, 1);\r
+ idx = key.substring(2);\r
+ var col = Math.floor((idx - 1) / numRows);\r
+ var row = (idx - 1) % numRows;\r
+ if (idx - numRows <= 0) row = numRows - row - 1;\r
+ var X1 = Math.round(X0 + dX * col + (lane - 1) * dL);\r
+ var Y1 = Math.round(Y0 + dY * row);\r
+ var X2 = Math.round(X1 + dX);\r
+ var Y2 = Math.round(Y1 + dY);\r
+ area.coords = "'" + X1 + "," + Y1 + "," + X2 + "," + Y2 + "'";\r
+ area.title = "L:" + lane + " T:" + idx + "\n" + "Val= " + val;\r
+ map.appendChild(area);\r
+ }\r
+ this.resetMap = function(image) {\r
+ if (image.id == imageOnFocusId) return;\r
+ xmlName = image.src;\r
+ xmlName = xmlName.replace("@.png", ".png");\r
+ xmlName = xmlName.substring(0, xmlName.lastIndexOf('.')) + ".xml";\r
+ var base = null;\r
+ if (xmlName.lastIndexOf('_a.xml') > 0) base = 'A';\r
+ else if (xmlName.lastIndexOf('_c.xml') > 0) base = 'C';\r
+ else if (xmlName.lastIndexOf('_g.xml') > 0) base = 'G';\r
+ else if (xmlName.lastIndexOf('_t.xml') > 0) base = 'T';\r
+ if (base != null) xmlName = xmlName.substring(0, xmlName.lastIndexOf('_')) + ".xml";\r
+ try {\r
+ this.tileMapXML = loadXMLDoc(xmlName);\r
+ layout = this.tileMapXML.getElementsByTagName("Layout");\r
+ if (layout != null && layout.length > 0) this.changeLayout(layout[0]);\r
+ tiles = this.tileMapXML.getElementsByTagName("TL");\r
+ while (map.lastChild != null) map.removeChild(map.lastChild);\r
+ for (i = 0; i < tiles.length; i++) tileMap.newToolTipVal(tiles[i], base);\r
+ } catch (e) { this.blankMap(); }\r
+ imageOnFocusId = image.id;\r
+ }\r
+\r
+\r
+ this.blankMap = function() {\r
+ while (map.lastChild != null) map.removeChild(map.lastChild);\r
+ for (var l = 1; l <= numLanes; l++) {\r
+ for (var i = 1; i <= numTiles; i++) {\r
+ this.newToolTip(l, i);\r
+ }\r
+ }\r
+ }\r
+}\r
+\r
+function fillCycles(CyBox, maxCy) {\r
+ for (var cy = 1; cy <= maxCy; cy++) {\r
+ var option = document.createElement('option');\r
+ option.setAttribute('value', cy);\r
+ option.appendChild(document.createTextNode(cy));\r
+ CyBox.appendChild(option);\r
+ }\r
+}\r
+\r
+function changeImage(form) {\r
+ var qc = form.QCOptDropDown.value;\r
+ var base = "";\r
+ var cycle = "";\r
+ //alert(form.autoscale.id);\r
+ //return;\r
+ if (form.baseDropDown != null) {\r
+ if (qc == "ErrorRate" || qc == "NumGT30") {\r
+ form.baseDropDown.style.display = 'none';\r
+ document.getElementById(form.autoscale.id.toString() + 'lbl').style.display = 'inline';\r
+ }\r
+ else {\r
+ form.baseDropDown.style.display = 'inline';\r
+ base = "_" + form.baseDropDown.value.toLowerCase();\r
+ document.getElementById(form.autoscale.id.toString() + 'lbl').style.display = 'none';\r
+\r
+ }\r
+ }\r
+ if (form.cyDropDown != null) {\r
+ form.cyDropDown.disabled = false;\r
+ if (form.cyDropDown != null && !form.cyDropDown.disabled) {\r
+ cycle = "_" + form.cyDropDown.value.toLowerCase();\r
+ qc = qc + "/";\r
+ }\r
+ } else qc = qc + "_";\r
+ auto = "";\r
+ if (form.autoscale.checked) auto = "@";\r
+ var suff = cycle + base + auto + ".png";\r
+ form.Chart.src = "../reports/" + qc + "Chart" + suff;\r
+ form.Chart.lowsrc = form.Chart.src;\r
+ imageOnFocusId = null;\r
+}\r
+\r
+function showBlank(imgId) {\r
+ document.getElementById(imgId).lowsrc = document.getElementById(imgId).src;\r
+ document.getElementById(imgId).src = "../reports/blank.png";\r
+}\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Controls.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="selected" href="./Controls.htm">Controls</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="ControlsTbl" ><p> No data available yet.</p></div>\r
+ <script type="text/javascript">loadControls()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function loadControls() {\r
+ loadXSLTable('../reports/controls.xml', './controls.xsl', 'ControlsTbl');\r
+}
\ No newline at end of file
--- /dev/null
+<?xml version="1.0"?> \r
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" \r
+version="1.0"> \r
+<xsl:output method="html" indent="yes" omit-xml-declaration="yes"/>\r
+<xsl:template match="/">\r
+ <table class="DataTable" >\r
+ <tr>\r
+ <th>Control</th>\r
+ <th >Lane 1</th><th >Lane 2</th><th >Lane 3</th><th >Lane 4</th>\r
+ <th >Lane 5</th><th >Lane 6</th><th >Lane 7</th><th >Lane 8</th>\r
+ </tr>\r
+ <xsl:for-each select="Controls/ctl"><tr>\r
+ <td><xsl:value-of select="@Key"/></td> \r
+ <td><xsl:value-of select="@L1"/></td> \r
+ <td><xsl:value-of select="@L2"/></td> \r
+ <td><xsl:value-of select="@L3"/></td> \r
+ <td><xsl:value-of select="@L4"/></td> \r
+ <td><xsl:value-of select="@L5"/></td> \r
+ <td><xsl:value-of select="@L6"/></td> \r
+ <td><xsl:value-of select="@L7"/></td> \r
+ <td><xsl:value-of select="@L8"/></td>\r
+ </tr></xsl:for-each>\r
+ </table >\r
+</xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<html xmlns="http://www.w3.org/1999/xhtml" >\r
+<head></head> \r
+<body>\r
+<p>There was a problem loading the file.</p>\r
+<p>Please click a link below to try again</p>\r
+<p><a href="..\Status.htm">Status.htm</a></p>\r
+</body>\r
+</html>\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a class="selected" href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <script type="text/javascript" >\r
+ loadXSLTable('../reports/Status.xml', './RunInfo.xsl', 'container');\r
+ </script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <table class="InfoTable">\r
+ <tr style="text-align: center;">Run Description<p/></tr>\r
+ <tr><th>Software:</th><td><xsl:value-of select="/Status/Software"/></td></tr>\r
+ <tr><th>Run name:</th><td><xsl:value-of select="/Status/RunName"/></td></tr>\r
+ <tr><th>Cycles:</th><td><xsl:value-of select="/Status/NumCycles"/></td></tr>\r
+ <tr><th>Instrument name:</th><td><xsl:value-of select="/Status/InstrumentName"/></td></tr>\r
+ <tr><th>Run Started (Estimated):</th><td><xsl:value-of select="/Status/RunStarted"/></td></tr>\r
+ <tr><th>Input Directory:</th><td><xsl:value-of select="/Status/InputDir"/></td></tr>\r
+ <tr><th>Output Directory:</th><td><xsl:value-of select="/Status/OutputDir"/></td></tr>\r
+ <tr><p/></tr>\r
+ </table >\r
+ <p/>\r
+ <table class="InfoTable">\r
+ <tr style="text-align: center;">Configuration Settings<p/></tr>\r
+ <tr><th><li type="square">Copy all run files:</li></th><td><xsl:value-of select="/Status/Configuration/CopyAllFiles"/></td></tr>\r
+ <tr><th><li type="square">Copy images:</li></th><td><xsl:value-of select="/Status/Configuration/CopyImages"/></td></tr>\r
+ <tr><th><li type="square">Delete image files:</li></th><td><xsl:value-of select="/Status/Configuration/DeleteImages"/></td></tr>\r
+ <tr><th><li type="square">Delete intensity files:</li></th><td><xsl:value-of select="/Status/Configuration/DeleteIntensity"/></td></tr>\r
+ <tr><th><li type="square">Run info file exists:</li></th><td><xsl:value-of select="/Status/Configuration/RunInfoExists"/></td></tr>\r
+ <tr><th><li type="square">Is this a paired end run:</li></th><td><xsl:value-of select="/Status/Configuration/IsPairedEndRun"/></td></tr>\r
+ <tr><th><li type="square">Total number of reads:</li></th><td><xsl:value-of select="/Status/Configuration/NumberOfReads"/></td></tr>\r
+ <tr><th><li type="square">Number of lanes:</li></th><td><xsl:value-of select="/Status/Configuration/NumberOfLanes"/></td></tr>\r
+ <tr><th><li type="square">Number of tiles per lane:</li></th><td><xsl:value-of select="/Status/Configuration/TilesPerLane"/></td></tr>\r
+ <tr><th><li type="square">Control lane:</li></th>\r
+ <td>\r
+ <xsl:if test="/Status/Configuration/ControlLane = 0"> None</xsl:if>\r
+ <xsl:if test="/Status/Configuration/ControlLane > 0 ">\r
+ <xsl:value-of select="/Status/Configuration/ControlLane"/>\r
+ </xsl:if>\r
+ </td>\r
+ </tr> \r
+ </table>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <xsl:value-of select="/Status/RunName"/>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+body\r
+{\r
+ margin: 0px;\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ background-color: #F4F5F5;\r
+ border-top-style: solid;\r
+ border-top-color: #FF9900;\r
+ border-top-width: 10px;\r
+ padding-top: 3px;\r
+ background-image: url('../Status_Files/illumina.png');\r
+ background-repeat: no-repeat;\r
+ background-position: top right;\r
+ color: #555;\r
+ font-weight: bold;\r
+}\r
+\r
+#tabmenu\r
+{\r
+ font: normal 14px Arial, Helvetica, sans-serif;\r
+ list-style-type: none;\r
+ border-bottom: 1px solid #BB5500;\r
+ margin: 12px 0px 0px 0px;\r
+ padding-left: 0;\r
+ padding-right: 0;\r
+ padding-bottom: 26px;\r
+ font-weight: bold;\r
+}\r
+\r
+#tabmenu li\r
+{\r
+ display: inline;\r
+ float: left;\r
+ height: 24px;\r
+ min-width: 80px;\r
+ text-align: center;\r
+ padding: 0;\r
+}\r
+\r
+#tabmenu li a\r
+{\r
+ float: left;\r
+ color: #777;\r
+ text-decoration: none;\r
+ padding: 4px;\r
+ text-align: center;\r
+ background-color: #ddd;\r
+ min-width: 80px;\r
+ border: 1px solid gray;\r
+ border-bottom: none;\r
+ margin: 0px 1px 0px 1px;\r
+\r
+}\r
+\r
+#tabmenu li a.selected\r
+{\r
+ background-color: #F7F8f8;\r
+ color: #000;\r
+ font-size: 100%;\r
+ border: 1px solid #BB5500;\r
+ border-bottom: 2px solid #F7F8f8;\r
+\r
+}\r
+\r
+#tabmenu li a:hover\r
+{\r
+ color: #BB5500;\r
+ font-size :120%;\r
+ border: 1px solid #BB5500;\r
+}\r
+#tabmenu li a.selected:hover\r
+{\r
+ border-bottom: 2px solid #F7F8f8;\r
+}\r
+\r
+#container\r
+{\r
+ border: 1px solid #BB5500;\r
+ border-top: none;\r
+ padding: 10px;\r
+ left: 0;\r
+ top: 0;\r
+ background-color: #F7F8f8;\r
+ min-width: 1100px;\r
+}\r
+\r
+\r
+\r
+#tabmenu li a.space\r
+{\r
+ font-weight: normal;\r
+ font-size :100%;\r
+ color: #000;\r
+ background-color: #F5F5F5;\r
+ border: none;\r
+ text-align: right;\r
+}\r
+\r
+table.DataTable\r
+{\r
+ border-collapse: collapse;\r
+ background-color: #e0e0e0;\r
+ border: 1px dotted #BB5500;\r
+ padding: 10px;\r
+ padding:50px;\r
+\r
+}\r
+\r
+table.DataTable td, table.DataTable th\r
+{\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ font-size: smaller;\r
+ font-weight: bold;\r
+ font-variant: normal;\r
+ text-transform: none;\r
+ padding: 3px; \r
+ border-right: dotted 1px #BB5500;\r
+ border-left: dotted 1px #BB5500;\r
+ color: #555555;\r
+}\r
+\r
+table.DataTable tr:hover td, table.DataTable tr:hover td a, table.DataTable tr:hover th a\r
+{\r
+ color: #BB5500;\r
+}\r
+\r
+table.DataTable th\r
+{\r
+ padding: 5px;\r
+ border: dotted 1px #BB5500;\r
+ color: #000000;\r
+}\r
+\r
+table.InfoTable\r
+{\r
+ margin: 20px;\r
+ border-style: none;\r
+ border-collapse: collapse;\r
+ background-color: #e0e0e0;\r
+ padding: 50px;\r
+ outline-style: solid;\r
+ outline-color: #e0e0e0;\r
+ outline-width: 10px;\r
+}\r
+\r
+table.InfoTable td, table.InfoTable th\r
+{\r
+ border-style: none;\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ font-size: smaller;\r
+ font-weight: bold;\r
+ font-variant: normal;\r
+ text-transform: none;\r
+ padding: 5px 30px 5px 20px;\r
+ color: #555555;\r
+ text-align: left;\r
+}\r
+\r
+table.InfoTable tr:hover td, table.InfoTable tr:hover td a, table.InfoTable tr:hover th a\r
+{\r
+ color: #BB5500;\r
+}\r
+\r
+table.InfoTable th\r
+{\r
+ color: #000000;\r
+}\r
+\r
+table.StatusTable\r
+{\r
+ margin: 0px 0px 0px 0px;\r
+ border-collapse: collapse;\r
+ background-color: #e0e0e0;\r
+ padding: 1px;\r
+ /*outline-style: solid;\r
+ outline-color: #e0e0e0;\r
+ outline-width: 2px;*/\r
+ border: 1px dotted #BB5500;\r
+\r
+}\r
+\r
+table.StatusTable td, table.StatusTable th\r
+{\r
+ border: 1px dotted #BB5500;\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ font-size: small;\r
+ font-weight: bold;\r
+ font-variant: normal;\r
+ text-transform: none;\r
+ color: #555555;\r
+ text-align: left;\r
+}\r
+table.StatusTable th\r
+{\r
+ border-right: none;\r
+ padding-right: 5px;\r
+}\r
+\r
+table.StatusTable td\r
+{\r
+ border-left: none;\r
+ padding-right: 5px;\r
+ color: #BB5500;\r
+}\r
+\r
+table.StatusTable tr:hover td, table.StatusTable tr:hover td a, table.StatusTable tr:hover th a\r
+{\r
+ color: #ff8800;\r
+}\r
+\r
+label\r
+{\r
+ font-size: smaller;\r
+ font-weight: normal;\r
+ color: #000000;\r
+}\r
+\r
+image.Chart\r
+{\r
+ border: 1px solid #BB5500;\r
+ margin: 5px 0px 0px 0px;\r
+}\r
+\r
+iframe\r
+{ \r
+ margin: 5px 0px 0px 0px;\r
+ border: 1px solid #BB5500;\r
+}\r
+\r
+#RunNameTD\r
+{font-size :100%; padding-left: 20px}
\ No newline at end of file
--- /dev/null
+window.onerror = function() {\r
+ parent.location = "./Status_Files/StatusError.htm"\r
+}\r
+\r
+//Reading XML file\r
+var xmlhttp = false;\r
+/* running locally on IE5.5, IE6, IE7 */; /*@cc_on\r
+if (location.protocol == "file:") {\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("MSXML2.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("Microsoft.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+}\r
+/* IE7, Firefox, Safari, Opera... */\r
+if (!xmlhttp) try { xmlhttp = new XMLHttpRequest(); } catch (e) { xmlhttp = false; }\r
+/* IE6 */\r
+if (typeof ActiveXObject != "undefined") {\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("MSXML2.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("Microsoft.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+}\r
+/* IceBrowser */\r
+if (!xmlhttp) try { xmlhttp = createRequest(); } catch (e) { xmlhttp = false; }\r
+\r
+function loadXMLDoc(dname) {\r
+ var xmlDoc = null;\r
+ try {\r
+ if (!xmlhttp) return "Your browser doesn't seem to support XMLHttpRequests.";\r
+ xmlhttp.open("GET", dname, false); //make sure open appears before onreadystatechange lest IE will encounter issues beyond the first request\r
+ xmlhttp.send(null);\r
+ var parser = false;\r
+ try {\r
+ parser = new DOMParser();\r
+ xmlDoc = parser.parseFromString(xmlhttp.responseText, "text/xml");\r
+ } catch (e) { parser = false }\r
+ if (!parser) {\r
+ xmlDoc = new ActiveXObject("Microsoft.XMLDOM");\r
+ //xmlDoc = new ActiveXObject("Msxml2.DOMDocument.6.0");\r
+ xmlDoc.async = "false";\r
+ xmlDoc.loadXML(xmlhttp.responseText);\r
+ }\r
+ if(xmlDoc.childNodes.length == 0)xmlDoc= null;\r
+ } catch(e){};\r
+ return xmlDoc;\r
+}\r
+//End of reading XML file\r
+\r
+\r
+function errorPrint(err) {\r
+ document.writeln(err.description);\r
+ document.writeln("<p>There was a problem loading the file.</p>");\r
+ document.writeln("<p>Please click a link below to try again</p>");\r
+ document.writeln("<p><a href='Status.htm'>Status.htm</a></p>");\r
+ }\r
+\r
+function imgRefresh(imgId) {\r
+ var s = document.getElementById(imgId).src;\r
+ if (s.indexOf('?') > 0) s = s.substring(0, s.indexOf('?'));\r
+ document.getElementById(imgId).src = s + "?" + (new Date().getMilliseconds());\r
+}\r
+\r
+function imgReload(imgId) {\r
+ document.getElementById(imgId).src = document.getElementById(imgId).lowsrc;\r
+}\r
+\r
+function getNodeText(node) {\r
+ var txt = "";\r
+ if (node.textContent != undefined) txt = node.textContent;\r
+ else if (node.text != undefined) txt = node.text;\r
+ return txt;\r
+}\r
+\r
+// Cookie functions\r
+function setCookie(name, value, expires, path, domain, secure) {\r
+ document.cookie = name + "=" + escape(value) +\r
+ ((expires) ? "; expires=" + expires.toGMTString() : "") +\r
+ ((path) ? "; path=" + path : "") +\r
+ ((domain) ? "; domain=" + domain : "") +\r
+ ((secure) ? "; secure" : "");\r
+}\r
+\r
+function getCookie(name) {\r
+ var dc = document.cookie;\r
+ var prefix = name + "=";\r
+ var begin = dc.indexOf("; " + prefix);\r
+ if (begin == -1) {\r
+ begin = dc.indexOf(prefix);\r
+ if (begin != 0) return null;\r
+ } else {\r
+ begin += 2;\r
+ }\r
+ var end = document.cookie.indexOf(";", begin);\r
+ if (end == -1) {\r
+ end = dc.length;\r
+ }\r
+ return unescape(dc.substring(begin + prefix.length, end));\r
+}\r
+\r
+function deleteCookie(name, path, domain) {\r
+ if (getCookie(name)) {\r
+ document.cookie = name + "=" +\r
+ ((path) ? "; path=" + path : "") +\r
+ ((domain) ? "; domain=" + domain : "") +\r
+ "; expires=Thu, 01-Jan-70 00:00:01 GMT";\r
+ }\r
+}\r
+\r
+function loadNumClustersTableByLane(xmlName, tblName, tagsName) {\r
+ tbl = document.getElementById(tblName);\r
+ xmlDoc = loadXMLDoc(xmlName);\r
+ if (xmlDoc == null) return;\r
+ xmlRows = xmlDoc.getElementsByTagName(tagsName);\r
+ while (tbl.rows.length > 0) tbl.deleteRow(tbl.rows.length - 1);\r
+ if (xmlRows.length > 0 && xmlRows[0].attributes.length > 0) {\r
+ for (i = 0; i < xmlRows.length; i++) {\r
+ tbl.insertRow(0);\r
+ for (j = xmlRows[i].attributes.length - 1; j >= 0; j--) {\r
+ tbl.rows[0].insertCell(0);\r
+ tbl.rows[0].cells[0].innerHTML = xmlRows[i].attributes[j].value;\r
+ }\r
+ //create column titles\r
+ tbl.insertRow(0);\r
+ }\r
+ for (j = xmlRows[0].attributes.length - 1; j >= 0; j--) {\r
+ tbl.rows[0].insertCell(0);\r
+ tbl.rows[0].cells[0].innerHTML = xmlRows[0].attributes[j].name;\r
+ }\r
+ tbl.rows[0].cells[0].innerHTML = tagsName + "#"\r
+ }\r
+}\r
+\r
+function loadXSLTable(xmlName, xslName, tblName) {\r
+ tbl = document.getElementById(tblName);\r
+ xmlDoc = loadXMLDoc(xmlName);\r
+ xslDoc = loadXMLDoc(xslName);\r
+ if (xmlDoc == null || xslDoc == null) return false;\r
+ // code for IE\r
+ if (window.ActiveXObject) {\r
+ ex = xmlDoc.transformNode(xslDoc);\r
+ tbl.innerHTML = ex;\r
+ }\r
+ // code for Mozilla, Firefox, Opera, etc.\r
+ else if (document.implementation && document.implementation.createDocument) {\r
+ xsltProcessor = new XSLTProcessor();\r
+ xsltProcessor.importStylesheet(xslDoc);\r
+ resultDocument = xsltProcessor.transformToFragment(xmlDoc, document);\r
+ if ( tbl.hasChildNodes() )\r
+ while ( tbl.childNodes.length >= 1 ) \r
+ tbl.removeChild( tbl.firstChild );\r
+ tbl.appendChild(resultDocument);\r
+ return true;\r
+ }\r
+}\r
+\r
+function xslTransform(xmlDoc, xslDoc) {\r
+ resultDocument = null;\r
+ if (xmlDoc != null && xslDoc != null) {\r
+ // code for IE\r
+ if (window.ActiveXObject) {\r
+ ex = xmlDoc.transformNode(xslDoc);\r
+ resultDocument = ex;\r
+ }\r
+ // code for Mozilla, Firefox, Opera, etc.\r
+ else if (document.implementation && document.implementation.createDocument) {\r
+ xsltProcessor = new XSLTProcessor();\r
+ xsltProcessor.importStylesheet(xslDoc);\r
+ resultDocument = xsltProcessor.transformToFragment(xmlDoc, document).textContent;\r
+ }\r
+ }\r
+ return resultDocument;\r
+}\r
--- /dev/null
+<html xmlns="http://www.w3.org/1999/xhtml" >\r
+<head></head> \r
+<body>\r
+<p>There was a problem loading the file.</p>\r
+<p>Please click a link below to try again</p>\r
+<p><a href=".\Status.htm">Status.htm</a></p>\r
+</body>\r
+</html>\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td id="NumCycles"><xsl:value-of select="/Status/NumCycles"/></td>\r
+ <th>Extracted:</th><td id="ImgCycle"><xsl:value-of select="/Status/ImgCycle"/></td>\r
+ <th>Called:</th><td id="CallCycle"><xsl:value-of select="/Status/CallCycle"/></td>\r
+ <th>Scored:</th><td id="ScoreCycle"><xsl:value-of select="/Status/ScoreCycle"/></td>\r
+ <th>Copied:</th><td id="CopyCycle"><xsl:value-of select="/Status/CopyCycle"/></td>\r
+ </tr></table>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Summary.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a class="selected" href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="SumTbl1" ><p> No data available yet.</p></div>\r
+ <div id="SumTbl2"></div>\r
+ <div id="SumTbl3"></div>\r
+ <div id="SumTbl4"></div>\r
+ <div id="SumTbl5"></div>\r
+ <div id="SumTbl6"></div>\r
+ <div id="SumTbl7"></div>\r
+ <div id="SumTbl8"></div>\r
+ <div id="SumTbl9"></div>\r
+ <div id="SumTbl10"></div>\r
+ <div id="SumTbl11"></div>\r
+ <script type="text/javascript">loadSumTable()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function loadSumTable() {\r
+ for (i = 1; i < 12; i++)\r
+ loadXSLTable('../reports/Summary/read' + i + '.xml', './Summary.xsl', 'SumTbl' + i);\r
+}
\ No newline at end of file
--- /dev/null
+<?xml version="1.0"?> \r
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" \r
+version="1.0"> \r
+<xsl:output method="html" indent="yes" omit-xml-declaration="yes"/>\r
+<xsl:template match="/">\r
+ <p/>   <b>Read #<xsl:value-of select="Summary/@Read"/></b>\r
+ <i><xsl:value-of select="Summary/@ReadType"/></i>\r
+ <table class="DataTable" >\r
+ <tr>\r
+ <th >Lane</th> <th>Tiles</th> <th>Clu.Dens. (#/mm<sup>2</sup>)</th>\r
+ <th>% PF Clusters </th> <th>Clusters PF (#/mm<sup>2</sup>)</th> <th>% Phas./Preph.</th>\r
+ <th>Cycles<br/>Err Rated</th> <th>% Aligned</th> <th>% Error Rate</th> \r
+ <th>% Error Rate<br/> 35 cycle</th > <th>% Error Rate<br/> 75 cycle</th > <th>% Error Rate<br/> 100 cycle</th > <th>1<sup>st</sup> Cycle Int</th>\r
+ <th>% Intensity<br/> Cycle 20</th>\r
+ </tr>\r
+ <xsl:variable name="densityRatio" select="Summary/@densityRatio"/>\r
+ <xsl:for-each select="Summary/Lane">\r
+ <tr>\r
+ <td><xsl:value-of select="@key"/></td> \r
+ <td><xsl:value-of select="@TileCount"/></td> \r
+ <td><xsl:value-of select="format-number(@ClustersRaw * $densityRatio div 1000,'#')"/>K +/- \r
+ <xsl:value-of select="format-number(@ClustersRawSD * $densityRatio div 1000,'#.0')"/>K</td> \r
+ <td><xsl:value-of select="@PrcPFClusters"/> +/- \r
+ <xsl:value-of select="@PrcPFClustersSD"/></td> \r
+ <td><xsl:value-of select="format-number(@ClustersPF* $densityRatio div 1000,'#.0')"/>K +/- \r
+ <xsl:value-of select="format-number(@ClustersPFSD* $densityRatio div 1000,'#.00')"/>K</td> \r
+ <td><xsl:value-of select="@Phasing"/> /\r
+ <xsl:value-of select="@Prephasing"/></td>\r
+ <td><xsl:value-of select="@CalledCyclesMin"/>\r
+ <xsl:if test="@CalledCyclesMax > @CalledCyclesMin">-<xsl:value-of select="@CalledCyclesMax"/></xsl:if></td>\r
+ <td><xsl:value-of select="@PrcAlign"/> +/-\r
+ <xsl:value-of select="@PrcAlignSD"/></td> \r
+ <td><xsl:value-of select="@ErrRatePhiX"/> +/-\r
+ <xsl:value-of select="@ErrRatePhiXSD"/></td>\r
+ <td><xsl:value-of select="@ErrRate35"/> +/-\r
+ <xsl:value-of select="@ErrRate35SD"/></td>\r
+ <td><xsl:value-of select="@ErrRate75"/> +/-\r
+ <xsl:value-of select="@ErrRate75SD"/></td>\r
+ <td><xsl:value-of select="@ErrRate100"/> +/-\r
+ <xsl:value-of select="@ErrRate100SD"/></td>\r
+ <td><xsl:value-of select="format-number(@FirstCycleIntPF,'#')"/> +/-\r
+ <xsl:value-of select="format-number(@FirstCycleIntPFSD,'#.0')"/></td>\r
+ <td><xsl:value-of select="format-number(@PrcIntensityAfter20CyclesPF,'#.0')"/> +/-\r
+ <xsl:value-of select="format-number(@PrcIntensityAfter20CyclesPFSD,'#.00')"/></td>\r
+ </tr>\r
+ </xsl:for-each>\r
+ </table >\r
+</xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <xsl:value-of select="/Status/Configuration/TilesPerLane"/>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Summary.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a class="selected" href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="SumTbl1" ><p> No data available yet.</p></div>\r
+ <div id="SumTbl2"></div>\r
+ <div id="SumTbl3"></div>\r
+ <div id="SumTbl4"></div>\r
+ <div id="SumTbl5"></div>\r
+ <div id="SumTbl6"></div>\r
+ <div id="SumTbl7"></div>\r
+ <div id="SumTbl8"></div>\r
+ <div id="SumTbl9"></div>\r
+ <div id="SumTbl10"></div>\r
+ <div id="SumTbl11"></div>\r
+ <script type="text/javascript">loadSumTable()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+<?xml version="1.0"?>
+<RunParameters>
+ <Barcodes>
+ </Barcodes>
+ <Defaults>
+ <ANALYSIS>none</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <CHROM_NAME_VALIDATION>on</CHROM_NAME_VALIDATION>
+ <CMDPREFIX></CMDPREFIX>
+ <DATASET_POST_RUN_COMMAND></DATASET_POST_RUN_COMMAND>
+ <ELAND_EXTENDED_MULTI_READS>off</ELAND_EXTENDED_MULTI_READS>
+ <ELAND_FASTQ_FILES_PER_PROCESS>3</ELAND_FASTQ_FILES_PER_PROCESS>
+ <ELAND_GENOME></ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_MAX_MATCHES></ELAND_MAX_MATCHES>
+ <ELAND_PARAMS></ELAND_PARAMS>
+ <ELAND_REPEAT></ELAND_REPEAT>
+ <ELAND_RNA_GENE_MD_GROUP_LABEL></ELAND_RNA_GENE_MD_GROUP_LABEL>
+ <ELAND_RNA_GENOME_ANNOTATION></ELAND_RNA_GENOME_ANNOTATION>
+ <ELAND_RNA_GENOME_CONTAM></ELAND_RNA_GENOME_CONTAM>
+ <ELAND_RNA_GENOME_CONTAM_MASK>*.fa</ELAND_RNA_GENOME_CONTAM_MASK>
+ <ELAND_RNA_MULTI_READS>off</ELAND_RNA_MULTI_READS>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <ELAND_SEED_LENGTH2></ELAND_SEED_LENGTH2>
+ <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
+ <EMAIL_LIST>${logName}</EMAIL_LIST>
+ <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
+ <EXPT_DIR>/mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM</EXPT_DIR>
+ <FLAT_TXT_GZ_SUFFIX>Flat.txt.gz</FLAT_TXT_GZ_SUFFIX>
+ <FLOWCELL>D07K6ACXX</FLOWCELL>
+ <GENE_MD_GZ_SUFFIX>_gene.md.gz</GENE_MD_GZ_SUFFIX>
+ <INCREASED_SENSITIVITY></INCREASED_SENSITIVITY>
+ <KAGU_PAIR_PARAMS>--muf 0</KAGU_PAIR_PARAMS>
+ <KAGU_PARAMS>--mmaq 4</KAGU_PARAMS>
+ <NUM_LEADING_DIRS_TO_STRIP>2</NUM_LEADING_DIRS_TO_STRIP>
+ <OA_SUFFIX>.oa</OA_SUFFIX>
+ <ORIGINAL_READS>1</ORIGINAL_READS>
+ <ORIGINAL_READ_LENGTH1>50</ORIGINAL_READ_LENGTH1>
+ <ORPHAN_ALIGNER_PARAMS>2</ORPHAN_ALIGNER_PARAMS>
+ <OUT_DIR>/mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM</OUT_DIR>
+ <PAS_PARAMS></PAS_PARAMS>
+ <RAMM_REPORT_TYPE></RAMM_REPORT_TYPE>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <RNAQC_COUNT_CLUSTERS_CMD>$(WC) -l</RNAQC_COUNT_CLUSTERS_CMD>
+ <RNAQC_COUNT_CLUSTERS_NAME>totalClusters</RNAQC_COUNT_CLUSTERS_NAME>
+ <RNAQC_COUNT_GENOME_CMD>($(GREP) -cvE '^((NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$|splice_sites)' || exit 0)</RNAQC_COUNT_GENOME_CMD>
+ <RNAQC_COUNT_GENOME_NAME>genomeUsable</RNAQC_COUNT_GENOME_NAME>
+ <RNAQC_COUNT_NM_CMD>($(FGREP) -wc NM || exit 0)</RNAQC_COUNT_NM_CMD>
+ <RNAQC_COUNT_NM_NAME>noMatch</RNAQC_COUNT_NM_NAME>
+ <RNAQC_COUNT_PF_CMD>$(WC) -l</RNAQC_COUNT_PF_CMD>
+ <RNAQC_COUNT_PF_NAME>PFClusters</RNAQC_COUNT_PF_NAME>
+ <RNAQC_COUNT_QC_CMD>($(FGREP) -wc QC || exit 0)</RNAQC_COUNT_QC_CMD>
+ <RNAQC_COUNT_QC_NAME>QC</RNAQC_COUNT_QC_NAME>
+ <RNAQC_COUNT_RM_CMD>($(FGREP) -wc RM || exit 0)</RNAQC_COUNT_RM_CMD>
+ <RNAQC_COUNT_RM_NAME>repeatMasked</RNAQC_COUNT_RM_NAME>
+ <RNAQC_COUNT_SPLICE_CMD>($(FGREP) -c splice_sites || exit 0)</RNAQC_COUNT_SPLICE_CMD>
+ <RNAQC_COUNT_SPLICE_NAME>spliceUsable</RNAQC_COUNT_SPLICE_NAME>
+ <RNAQC_COUNT_USABLE_CMD>$(CUT) -f13 |($(EGREP) [0-9] || exit 0)|$(WC) -l</RNAQC_COUNT_USABLE_CMD>
+ <RNAQC_COUNT_USABLE_NAME>usable</RNAQC_COUNT_USABLE_NAME>
+ <RNAQC_FIND_CONTAMS_CMD>($(GREP) -vE '^(NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$' || exit 0)</RNAQC_FIND_CONTAMS_CMD>
+ <SAMTOOLS_GENOME></SAMTOOLS_GENOME>
+ <SEQGENEMD2REFFLAT_PARAMS></SEQGENEMD2REFFLAT_PARAMS>
+ <SINGLESEED></SINGLESEED>
+ <SPLCSTS_PARAMS>-v $(CASAVA_LOG_LEVEL)</SPLCSTS_PARAMS>
+ <SQUASH_GENOME_PARAMS></SQUASH_GENOME_PARAMS>
+ <UNGAPPED></UNGAPPED>
+ <USE_BASES>y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
+ <WITH_ORPHAN_ALIGNER>true</WITH_ORPHAN_ALIGNER>
+ </Defaults>
+ <Lanes>
+ <Lane index="1">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
+ <Lane index="2">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
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+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Reference>
+ </References>
+ <Samples>
+ </Samples>
+ <Software CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureAlignment.pl config.txt --EXPT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM/ --OUT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM -make" Name="configureAlignment.pl" Version="CASAVA-1.8.1">
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+ <Software Name="RTA" Version="1.12.4.2">
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+ </Software>
+ </Software>
+ </Software>
+ </Software>
+</RunParameters>
--- /dev/null
+<DemultiplexConfig>
+ <Software Version="CASAVA-1.8.1" CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls/ --output-dir Unaligned --sample-sheet Data/Intensities/BaseCalls/SampleSheet.csv" Name="configureBclToFastq.pl">
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--- /dev/null
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+</BaseCallAnalysis>
--- /dev/null
+<?xml version="1.0"?>
+<BustardSummary>
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+ <clusterCountRaw>781064977</clusterCountRaw>
+ <yield>25888586667</yield>
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+ <ChipSummary>
+ <ChipID>unknown</ChipID>
+ <Machine>HWI-ST0787</Machine>
+ <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
+ </ChipSummary>
+ <Date>2011-08-18 20:18:19</Date>
+ <ExpandedLaneSummary>
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+ </Tile>
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+ </Tile>
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+ <tileNumber>1208</tileNumber>
+ </Tile>
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+ <tileNumber>1301</tileNumber>
+ </Tile>
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+ </Tile>
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+ </Tile>
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+ </Tile>
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+ </Tile>
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+ <signal20AsPctOf1>86.97</signal20AsPctOf1>
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+ </Tile>
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+ <tileNumber>1307</tileNumber>
+ </Tile>
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+ <signal20AsPctOf1>83.85</signal20AsPctOf1>
+ <tileNumber>1308</tileNumber>
+ </Tile>
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+ <signal20AsPctOf1>90.01</signal20AsPctOf1>
+ <tileNumber>2101</tileNumber>
+ </Tile>
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+ <signal20AsPctOf1>90.66</signal20AsPctOf1>
+ <tileNumber>2102</tileNumber>
+ </Tile>
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+ <signal20AsPctOf1>90.66</signal20AsPctOf1>
+ <tileNumber>2103</tileNumber>
+ </Tile>
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+ <tileNumber>2104</tileNumber>
+ </Tile>
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+ </Tile>
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+ </Tile>
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+ <tileNumber>2107</tileNumber>
+ </Tile>
+ <Tile>
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+ <percentClustersPF>66.93</percentClustersPF>
+ <signal20AsPctOf1>87.34</signal20AsPctOf1>
+ <tileNumber>2108</tileNumber>
+ </Tile>
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+ <percentClustersPF>92.31</percentClustersPF>
+ <signal20AsPctOf1>88.49</signal20AsPctOf1>
+ <tileNumber>2201</tileNumber>
+ </Tile>
+ <Tile>
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+ <percentClustersPF>91.87</percentClustersPF>
+ <signal20AsPctOf1>89.42</signal20AsPctOf1>
+ <tileNumber>2202</tileNumber>
+ </Tile>
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+ <tileNumber>2203</tileNumber>
+ </Tile>
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+ <tileNumber>2204</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4372303</clusterCountPF>
+ <clusterCountRaw>4862284</clusterCountRaw>
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+ <percentClustersPF>89.92</percentClustersPF>
+ <signal20AsPctOf1>88.76</signal20AsPctOf1>
+ <tileNumber>2205</tileNumber>
+ </Tile>
+ <Tile>
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+ <clusterCountRaw>5119662</clusterCountRaw>
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+ <signal20AsPctOf1>88.81</signal20AsPctOf1>
+ <tileNumber>2206</tileNumber>
+ </Tile>
+ <Tile>
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+ <clusterCountRaw>5301292</clusterCountRaw>
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+ <signal20AsPctOf1>89.46</signal20AsPctOf1>
+ <tileNumber>2207</tileNumber>
+ </Tile>
+ <Tile>
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+ <clusterCountRaw>5523881</clusterCountRaw>
+ <oneSig>1328.04</oneSig>
+ <percentClustersPF>67.85</percentClustersPF>
+ <signal20AsPctOf1>85.54</signal20AsPctOf1>
+ <tileNumber>2208</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3685991</clusterCountPF>
+ <clusterCountRaw>4034260</clusterCountRaw>
+ <oneSig>1437.04</oneSig>
+ <percentClustersPF>91.37</percentClustersPF>
+ <signal20AsPctOf1>88.87</signal20AsPctOf1>
+ <tileNumber>2301</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3894450</clusterCountPF>
+ <clusterCountRaw>4285846</clusterCountRaw>
+ <oneSig>1425.73</oneSig>
+ <percentClustersPF>90.87</percentClustersPF>
+ <signal20AsPctOf1>89.86</signal20AsPctOf1>
+ <tileNumber>2302</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3941822</clusterCountPF>
+ <clusterCountRaw>4382141</clusterCountRaw>
+ <oneSig>1397.98</oneSig>
+ <percentClustersPF>89.95</percentClustersPF>
+ <signal20AsPctOf1>90.41</signal20AsPctOf1>
+ <tileNumber>2303</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4299760</clusterCountPF>
+ <clusterCountRaw>4825173</clusterCountRaw>
+ <oneSig>1380.92</oneSig>
+ <percentClustersPF>89.11</percentClustersPF>
+ <signal20AsPctOf1>89.99</signal20AsPctOf1>
+ <tileNumber>2304</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4523197</clusterCountPF>
+ <clusterCountRaw>5101827</clusterCountRaw>
+ <oneSig>1374.81</oneSig>
+ <percentClustersPF>88.66</percentClustersPF>
+ <signal20AsPctOf1>89.72</signal20AsPctOf1>
+ <tileNumber>2305</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4658536</clusterCountPF>
+ <clusterCountRaw>5357124</clusterCountRaw>
+ <oneSig>1362.66</oneSig>
+ <percentClustersPF>86.96</percentClustersPF>
+ <signal20AsPctOf1>88.93</signal20AsPctOf1>
+ <tileNumber>2306</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4706753</clusterCountPF>
+ <clusterCountRaw>5569616</clusterCountRaw>
+ <oneSig>1336.27</oneSig>
+ <percentClustersPF>84.51</percentClustersPF>
+ <signal20AsPctOf1>89.15</signal20AsPctOf1>
+ <tileNumber>2307</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>2196707</clusterCountPF>
+ <clusterCountRaw>3787138</clusterCountRaw>
+ <oneSig>1265.29</oneSig>
+ <percentClustersPF>58.00</percentClustersPF>
+ <signal20AsPctOf1>89.55</signal20AsPctOf1>
+ <tileNumber>2308</tileNumber>
+ </Tile>
+ <readNumber>1</readNumber>
+ </Read>
+
+ <laneNumber>8</laneNumber>
+ </Lane>
+ </TileResultsByLane>
+</BustardSummary>
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<!--Illumina RTA Status Report-->\r
+<Status>\r
+ <Software>Illumina RTA 1.12.4.2</Software>\r
+ <RunName>110815_SN787_0101_AD07K6ACXX</RunName>\r
+ <InstrumentName>HWI-ST0787</InstrumentName>\r
+ <RunStarted>Thursday, August 18, 2011 12:33 PM</RunStarted>\r
+ <NumCycles>57</NumCycles>\r
+ <ImgCycle>57</ImgCycle>\r
+ <ScoreCycle>57</ScoreCycle>\r
+ <CallCycle>57</CallCycle>\r
+ <InputDir>D:\Illumina\HiSeqTemp\110815_SN787_0101_AD07K6ACXX</InputDir>\r
+ <OutputDir>\\NICODEMUS\volvox\110815_SN787_0101_AD07K6ACXX</OutputDir>\r
+ <Configuration>\r
+ <CopyAllFiles>true</CopyAllFiles>\r
+ <CopyImages>False</CopyImages>\r
+ <DeleteImages>True</DeleteImages>\r
+ <RunInfoExists>True</RunInfoExists>\r
+ <IsPairedEndRun>False</IsPairedEndRun>\r
+ <NumberOfReads>2</NumberOfReads>\r
+ <NumberOfLanes>8</NumberOfLanes>\r
+ <TilesPerLane>48</TilesPerLane>\r
+ <ControlLane>0</ControlLane>\r
+ </Configuration>\r
+</Status>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?><!--Illumina RTA Status Report--><Status><NumCycles>57</NumCycles><ImgCycle>57</ImgCycle><ScoreCycle>57</ScoreCycle><CopyCycle>57</CopyCycle><CallCycle>57</CallCycle><ErrRateCycle>57</ErrRateCycle></Status>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?><!--Illumina RTA Data--><Summary Read="1" densityRatio="0.173619792"><Lane key="1" TileCount="48" ClustersRaw="3878755" ClustersRawSD="579626.0" ClustersPF="1040253" ClustersPFSD="1059982.5" PrcPFClusters="27.8" PrcPFClustersSD="27.72" Phasing="0.381" Prephasing="0.084" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="707" FirstCycleIntPFSD="2076.1" PrcIntensityAfter20CyclesPF="60.0" PrcIntensityAfter20CyclesPFSD="6.61" /><Lane key="2" TileCount="48" ClustersRaw="3920639" ClustersRawSD="1027332.4" ClustersPF="474380" ClustersPFSD="739312.7" PrcPFClusters="13.4" PrcPFClustersSD="17.58" Phasing="0.369" Prephasing="0.251" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="2617" FirstCycleIntPFSD="3391.7" PrcIntensityAfter20CyclesPF="60.0" PrcIntensityAfter20CyclesPFSD="5.30" /><Lane key="3" TileCount="48" ClustersRaw="5713049" ClustersRawSD="876187.3" ClustersPF="376501" ClustersPFSD="895452.3" PrcPFClusters="6.0" PrcPFClustersSD="14.30" Phasing="0.247" Prephasing="0.200" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="5279" FirstCycleIntPFSD="1974.8" PrcIntensityAfter20CyclesPF="21.8" PrcIntensityAfter20CyclesPFSD="35.10" /><Lane key="4" TileCount="48" ClustersRaw="5852907" ClustersRawSD="538640.6" ClustersPF="329831" ClustersPFSD="758370.9" PrcPFClusters="5.4" PrcPFClustersSD="12.52" Phasing="0.210" Prephasing="0.180" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="4181" FirstCycleIntPFSD="1283.3" PrcIntensityAfter20CyclesPF="29.0" PrcIntensityAfter20CyclesPFSD="45.34" /><Lane key="5" TileCount="48" ClustersRaw="4006751" ClustersRawSD="1265247.4" ClustersPF="52186" ClustersPFSD="233275.6" PrcPFClusters="0.9" PrcPFClustersSD="4.22" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="2579" FirstCycleIntPFSD="2952.5" PrcIntensityAfter20CyclesPF="16.0" PrcIntensityAfter20CyclesPFSD="29.57" /><Lane key="6" TileCount="48" ClustersRaw="5678021" ClustersRawSD="627070.7" ClustersPF="1490900" ClustersPFSD="1624380.0" PrcPFClusters="25.5" PrcPFClustersSD="26.81" Phasing="0.267" Prephasing="0.212" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="6221" FirstCycleIntPFSD="675.5" PrcIntensityAfter20CyclesPF="76.9" PrcIntensityAfter20CyclesPFSD="4.87" /><Lane key="7" TileCount="48" ClustersRaw="1854131" ClustersRawSD="429053.2" ClustersPF="1585131" ClustersPFSD="693768.5" PrcPFClusters="85.0" PrcPFClustersSD="30.78" Phasing="0.133" Prephasing="0.241" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="6584" FirstCycleIntPFSD="455.9" PrcIntensityAfter20CyclesPF="109.1" PrcIntensityAfter20CyclesPFSD="4.78" /><Lane key="8" TileCount="48" ClustersRaw="4777517" ClustersRawSD="592904.0" ClustersPF="4113021" ClustersPFSD="439623.7" PrcPFClusters="86.5" PrcPFClustersSD="7.36" Phasing="0.219" Prephasing="0.235" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="6314" FirstCycleIntPFSD="760.7" PrcIntensityAfter20CyclesPF="37.3" PrcIntensityAfter20CyclesPFSD="9.19" /></Summary>
\ No newline at end of file
--- /dev/null
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--- /dev/null
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\ No newline at end of file
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\ No newline at end of file
+++ /dev/null
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- <script src="./Summary.js" type="text/javascript"></script>\r
- <title>Status</title>\r
-</head>\r
- \r
-<body>\r
- <table style="border:none"><tr>\r
- <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
- <td id="StatUpdateDiv" >\r
- <table class="StatusTable"><tr>\r
- <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
- <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
- </tr></table></td> \r
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- </tr></table>\r
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- document.getElementById("RunNameTD").innerHTML = runName;\r
- document.title = runName + " Status";\r
- </script>\r
-<ul id="tabmenu">\r
- <li><a href="./RunInfo.htm">Run Info</a></li>\r
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- \r
-<div id="container">\r
- <div id="SumTbl1" ><p> No data available yet.</p></div>\r
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-</html>\r
-\r
+++ /dev/null
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-<RunParameters>
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- <ANALYSIS>none</ANALYSIS>
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- <CHROM_NAME_VALIDATION>on</CHROM_NAME_VALIDATION>
- <CMDPREFIX></CMDPREFIX>
- <DATASET_POST_RUN_COMMAND></DATASET_POST_RUN_COMMAND>
- <ELAND_EXTENDED_MULTI_READS>off</ELAND_EXTENDED_MULTI_READS>
- <ELAND_FASTQ_FILES_PER_PROCESS>3</ELAND_FASTQ_FILES_PER_PROCESS>
- <ELAND_GENOME></ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_MAX_MATCHES></ELAND_MAX_MATCHES>
- <ELAND_PARAMS></ELAND_PARAMS>
- <ELAND_REPEAT></ELAND_REPEAT>
- <ELAND_RNA_GENE_MD_GROUP_LABEL></ELAND_RNA_GENE_MD_GROUP_LABEL>
- <ELAND_RNA_GENOME_ANNOTATION></ELAND_RNA_GENOME_ANNOTATION>
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- <ELAND_RNA_MULTI_READS>off</ELAND_RNA_MULTI_READS>
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- <ELAND_SEED_LENGTH2></ELAND_SEED_LENGTH2>
- <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
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- <GENE_MD_GZ_SUFFIX>_gene.md.gz</GENE_MD_GZ_SUFFIX>
- <INCREASED_SENSITIVITY></INCREASED_SENSITIVITY>
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- <KAGU_PARAMS>--mmaq 4</KAGU_PARAMS>
- <NUM_LEADING_DIRS_TO_STRIP>2</NUM_LEADING_DIRS_TO_STRIP>
- <OA_SUFFIX>.oa</OA_SUFFIX>
- <ORIGINAL_READS>1</ORIGINAL_READS>
- <ORIGINAL_READ_LENGTH1>50</ORIGINAL_READ_LENGTH1>
- <ORPHAN_ALIGNER_PARAMS>2</ORPHAN_ALIGNER_PARAMS>
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- <RAMM_REPORT_TYPE></RAMM_REPORT_TYPE>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <RNAQC_COUNT_CLUSTERS_CMD>$(WC) -l</RNAQC_COUNT_CLUSTERS_CMD>
- <RNAQC_COUNT_CLUSTERS_NAME>totalClusters</RNAQC_COUNT_CLUSTERS_NAME>
- <RNAQC_COUNT_GENOME_CMD>($(GREP) -cvE '^((NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$|splice_sites)' || exit 0)</RNAQC_COUNT_GENOME_CMD>
- <RNAQC_COUNT_GENOME_NAME>genomeUsable</RNAQC_COUNT_GENOME_NAME>
- <RNAQC_COUNT_NM_CMD>($(FGREP) -wc NM || exit 0)</RNAQC_COUNT_NM_CMD>
- <RNAQC_COUNT_NM_NAME>noMatch</RNAQC_COUNT_NM_NAME>
- <RNAQC_COUNT_PF_CMD>$(WC) -l</RNAQC_COUNT_PF_CMD>
- <RNAQC_COUNT_PF_NAME>PFClusters</RNAQC_COUNT_PF_NAME>
- <RNAQC_COUNT_QC_CMD>($(FGREP) -wc QC || exit 0)</RNAQC_COUNT_QC_CMD>
- <RNAQC_COUNT_QC_NAME>QC</RNAQC_COUNT_QC_NAME>
- <RNAQC_COUNT_RM_CMD>($(FGREP) -wc RM || exit 0)</RNAQC_COUNT_RM_CMD>
- <RNAQC_COUNT_RM_NAME>repeatMasked</RNAQC_COUNT_RM_NAME>
- <RNAQC_COUNT_SPLICE_CMD>($(FGREP) -c splice_sites || exit 0)</RNAQC_COUNT_SPLICE_CMD>
- <RNAQC_COUNT_SPLICE_NAME>spliceUsable</RNAQC_COUNT_SPLICE_NAME>
- <RNAQC_COUNT_USABLE_CMD>$(CUT) -f13 |($(EGREP) [0-9] || exit 0)|$(WC) -l</RNAQC_COUNT_USABLE_CMD>
- <RNAQC_COUNT_USABLE_NAME>usable</RNAQC_COUNT_USABLE_NAME>
- <RNAQC_FIND_CONTAMS_CMD>($(GREP) -vE '^(NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$' || exit 0)</RNAQC_FIND_CONTAMS_CMD>
- <SAMTOOLS_GENOME></SAMTOOLS_GENOME>
- <SEQGENEMD2REFFLAT_PARAMS></SEQGENEMD2REFFLAT_PARAMS>
- <SINGLESEED></SINGLESEED>
- <SPLCSTS_PARAMS>-v $(CASAVA_LOG_LEVEL)</SPLCSTS_PARAMS>
- <SQUASH_GENOME_PARAMS></SQUASH_GENOME_PARAMS>
- <UNGAPPED></UNGAPPED>
- <USE_BASES>y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
- <WITH_ORPHAN_ALIGNER>true</WITH_ORPHAN_ALIGNER>
- </Defaults>
- <Lanes>
- <Lane index="1">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="2">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="4">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="5">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="6">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="7">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>none</ANALYSIS>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="8">
- <Barcodes></Barcodes>
- <Defaults>
- <ANALYSIS>none</ANALYSIS>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- <Lane index="3">
- <Barcodes></Barcodes>
- <Defaults>
- <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
- </Defaults>
- <Projects></Projects>
- <References></References>
- <Samples></Samples>
- </Lane>
- </Lanes>
- <Projects>
- <Project name="12383">
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Project>
- <Project name="Undetermined_indices">
- <ANALYSIS>none</ANALYSIS>
- </Project>
- </Projects>
- <References>
- <Reference name="mm9">
- <ANALYSIS>eland_extended</ANALYSIS>
- <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
- <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/mm9/chromosomes/</ELAND_GENOME>
- <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <READS>1</READS>
- <READ_LENGTH1>49</READ_LENGTH1>
- <USE_BASES>Y*n</USE_BASES>
- <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
- </Reference>
- </References>
- <Samples>
- </Samples>
- <Software CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureAlignment.pl config.txt --EXPT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM/ --OUT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM -make" Name="configureAlignment.pl" Version="CASAVA-1.8.1">
- <Software CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls/ --output-dir Unaligned_1MM --sample-sheet Data/Intensities/BaseCalls/SampleSheet.csv --mismatches 1" Name="configureBclToFastq.pl" Version="CASAVA-1.8.1">
- <Software Name="RTA" Version="1.12.4.2">
- <Software Name="RTA" Version="1.12.4.2">
- <Software Name="HiSeq Control Software" Platform="HiSeq" Version="1.4.8" />
- </Software>
- </Software>
- </Software>
- </Software>
-</RunParameters>
+++ /dev/null
-<DemultiplexConfig>
- <Software Version="CASAVA-1.8.1" CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls/ --output-dir Unaligned --sample-sheet Data/Intensities/BaseCalls/SampleSheet.csv" Name="configureBclToFastq.pl">
- <Software Version="1.12.4.2" Name="RTA">
- <Software Version="1.12.4.2" Name="RTA">
- <Software Version="1.4.8" Platform="HiSeq" Name="HiSeq Control Software" />
- </Software>
- </Software>
- </Software>
- <FlowcellInfo ID="D07K6ACXX" Operator="Lorian" Recipe="SR_indexing" Desc="">
- <Lane Number="1">
- <Sample ProjectId="12281" Control="N" Index="ACAGTG" SampleId="12281" Desc="Index #5 AWCon cell#3_N2" Ref="elegans190" />
- <Sample ProjectId="12279" Control="N" Index="CGATGT" SampleId="12279" Desc="Index #2 AWCon cell#1_N2" Ref="elegans190" />
- <Sample ProjectId="12280" Control="N" Index="TGACCA" SampleId="12280" Desc="Index #4 AWCon cell#2_N2" Ref="elegans190" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane1" Desc="Clusters with unmatched barcodes for lane 1" Ref="unknown" />
- </Lane>
- <Lane Number="2">
- <Sample ProjectId="12345" Control="N" Index="ACAGTG" SampleId="12345" Desc="Index #5 3 AWC ablated CX3695" Ref="elegans190" />
- <Sample ProjectId="12283" Control="N" Index="CAGATC" SampleId="12283" Desc="Index #7 AWCon cell#5_N2" Ref="elegans190" />
- <Sample ProjectId="12282" Control="N" Index="GCCAAT" SampleId="12282" Desc="Index #6 AWCon cell#4_N2" Ref="elegans190" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane2" Desc="Clusters with unmatched barcodes for lane 2" Ref="unknown" />
- </Lane>
- <Lane Number="3">
- <Sample ProjectId="12331" Control="N" Index="ACAGTG" SampleId="12331" Desc="Index #5 060111 FLDN2b(d8.5) H3K4me3 ChIP" Ref="mm9" />
- <Sample ProjectId="12383" Control="N" Index="CGATGT" SampleId="12383" Desc="Index #2 jwp ix-65 ni 16h" Ref="hg18" />
- <Sample ProjectId="12330" Control="N" Index="TGACCA" SampleId="12330" Desc="Index #4 060111 Bcl11bKO DL4 FLDN2a H3K4me3 ChIP" Ref="mm9" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane3" Desc="Clusters with unmatched barcodes for lane 3" Ref="unknown" />
- </Lane>
- <Lane Number="4">
- <Sample ProjectId="12385" Control="N" Index="ACAGTG" SampleId="12385" Desc="Index #5 jwp ix-65 i 16h" Ref="hg18" />
- <Sample ProjectId="12386" Control="N" Index="GCCAAT" SampleId="12386" Desc="Index #6 jwp ix-71 NI 16h" Ref="hg18" />
- <Sample ProjectId="12384" Control="N" Index="TGACCA" SampleId="12384" Desc="index #4 jwp ix-65 RD 16h" Ref="hg18" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane4" Desc="Clusters with unmatched barcodes for lane 4" Ref="unknown" />
- </Lane>
- <Lane Number="5">
- <Sample ProjectId="12387" Control="N" Index="CAGATC" SampleId="12387" Desc="Index #7 jwp ix-71 RD 16h" Ref="hg18" />
- <Sample ProjectId="12388" Control="N" Index="CTTGTA" SampleId="12388" Desc="Index #12 jwp ix-71 i 16h" Ref="hg18" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane5" Desc="Clusters with unmatched barcodes for lane 5" Ref="unknown" />
- </Lane>
- <Lane Number="6">
- <Sample ProjectId="12391" Control="N" Index="ACTTGA" SampleId="12391" Desc="Index #8 jwp ix-63 NI 4h" Ref="hg18" />
- <Sample ProjectId="12392" Control="N" Index="GATCAG" SampleId="12392" Desc="Index #9 jwp ix-63 DHT 10uM PA 4h" Ref="hg18" />
- <Sample ProjectId="12393" Control="N" Index="TAGCTT" SampleId="12393" Desc="Index #10 jwp ix-63 DHT 4h" Ref="hg18" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane6" Desc="Clusters with unmatched barcodes for lane 6" Ref="unknown" />
- </Lane>
- <Lane Number="7">
- <Sample ProjectId="12348_Index5" Control="N" Index="ACAGTG" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index8" Control="N" Index="ACTTGA" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index1" Control="N" Index="ATCACG" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index7" Control="N" Index="CAGATC" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index2" Control="N" Index="CGATGT" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index9" Control="N" Index="GATCAG" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index6" Control="N" Index="GCCAAT" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index4" Control="N" Index="TGACCA" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="12348_Index3" Control="N" Index="TTAGGC" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane7" Desc="Clusters with unmatched barcodes for lane 7" Ref="unknown" />
- </Lane>
- <Lane Number="8">
- <Sample ProjectId="12382_Index5" Control="N" Index="ACAGTG" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index8" Control="N" Index="ACTTGA" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index1" Control="N" Index="ATCACG" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index7" Control="N" Index="CAGATC" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index2" Control="N" Index="CGATGT" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index9" Control="N" Index="GATCAG" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index6" Control="N" Index="GCCAAT" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index10" Control="N" Index="TAGCTT" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index4" Control="N" Index="TGACCA" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="12382_Index3" Control="N" Index="TTAGGC" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
- <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane8" Desc="Clusters with unmatched barcodes for lane 8" Ref="unknown" />
- </Lane>
- </FlowcellInfo>
-</DemultiplexConfig>
+++ /dev/null
-<?xml version="1.0"?>
-<BaseCallAnalysis xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
- <Run Name="BaseCalls">
- <BaseCallParameters>
- <ChastityThreshold>0.6</ChastityThreshold>
- <Matrix Path="">
- <AutoFlag>2</AutoFlag>
- <AutoLane>0</AutoLane>
- <Cycle>1</Cycle>
- <CycleOffset>0</CycleOffset>
- <FirstCycle>1</FirstCycle>
- <LastCycle>50</LastCycle>
- <Read>1</Read>
- </Matrix>
- <Matrix Path="">
- <AutoFlag>2</AutoFlag>
- <AutoLane>0</AutoLane>
- <Cycle>51</Cycle>
- <CycleOffset>0</CycleOffset>
- <FirstCycle>51</FirstCycle>
- <LastCycle>57</LastCycle>
- <Read>2</Read>
- </Matrix>
- <Phasing Path="">
- <AutoFlag>2</AutoFlag>
- <AutoLane>0</AutoLane>
- <Cycle>2</Cycle>
- <CycleOffset>1</CycleOffset>
- <FirstCycle>1</FirstCycle>
- <LastCycle>50</LastCycle>
- <PhasingRate>0</PhasingRate>
- <PrephasingRate>0</PrephasingRate>
- <Read>1</Read>
- </Phasing>
- <Phasing Path="">
- <AutoFlag>2</AutoFlag>
- <AutoLane>0</AutoLane>
- <Cycle>52</Cycle>
- <CycleOffset>1</CycleOffset>
- <FirstCycle>51</FirstCycle>
- <LastCycle>57</LastCycle>
- <PhasingRate>0</PhasingRate>
- <PrephasingRate>0</PrephasingRate>
- <Read>2</Read>
- </Phasing>
- <PureBases>0</PureBases>
- <SmtFilter>failed-chastity</SmtFilter>
- <SmtRelation>le</SmtRelation>
- <SmtThreshold>1.0</SmtThreshold>
- </BaseCallParameters>
- <Cycles First="1" Last="57" Number="57"/>
- <RunParameters>
- <AutoCycleFlag>0</AutoCycleFlag>
- <Barcode>
- <Cycle Use="true">51</Cycle>
- <Cycle Use="true">52</Cycle>
- <Cycle Use="true">53</Cycle>
- <Cycle Use="true">54</Cycle>
- <Cycle Use="true">55</Cycle>
- <Cycle Use="true">56</Cycle>
- <Cycle Use="true">57</Cycle>
- </Barcode>
- <BasecallFlag>0</BasecallFlag>
- <Deblocked>0</Deblocked>
- <DebugFlag>0</DebugFlag>
- <FirstRunOnlyFlag>0</FirstRunOnlyFlag>
- <ImagingReads Index="1">
- <FirstCycle>1</FirstCycle>
- <LastCycle>50</LastCycle>
- </ImagingReads>
- <ImagingReads Index="2">
- <FirstCycle>51</FirstCycle>
- <LastCycle>57</LastCycle>
- <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
- </ImagingReads>
- <Instrument>HWI-ST0787</Instrument>
- <IterativeMatrixFlag>0</IterativeMatrixFlag>
- <MakeFlag>0</MakeFlag>
- <MaxCycle>0</MaxCycle>
- <MinCycle>0</MinCycle>
- <QTableVersion>New6</QTableVersion>
- <RunFlowcellId>D07K6ACXX</RunFlowcellId>
- <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
- <RunFolderDate>110815</RunFolderDate>
- <RunFolderId>0101</RunFolderId>
- <Reads Index="1">
- <FirstCycle>1</FirstCycle>
- <LastCycle>50</LastCycle>
- </Reads>
- </RunParameters>
- <Software Name="RTA" Version="1.12.4.2"/>
- <TileSelection>
- <Lane Index="1">
- <Sample>s</Sample>
- <Tile>1102</Tile>
- <Tile>1101</Tile>
- <Tile>1103</Tile>
- <Tile>1106</Tile>
- <Tile>1104</Tile>
- <Tile>1105</Tile>
- <Tile>1108</Tile>
- <Tile>1107</Tile>
- <Tile>1202</Tile>
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+++ /dev/null
-<?xml version="1.0"?>
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- <Tile>1305</Tile>\r
- <Tile>1203</Tile>\r
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- <Tile>2205</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2206</Tile>\r
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- <Tile>2302</Tile>\r
- <Tile>2107</Tile>\r
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- <Tile>2203</Tile>\r
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- <Tile>2303</Tile>\r
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- <Tile>1104</Tile>\r
- <Tile>1108</Tile>\r
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- <Tile>2104</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- <Lane Index="8">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2307</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- </TileSelection>\r
- <Time />\r
- <User />\r
- </Run>\r
-</ImageAnalysis>
\ No newline at end of file
projects / htsworkflow.git / commitdiff
