From c22c060d6a8a73b49de37f952d72e77f09aef199 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Fri, 23 Apr 2010 22:21:46 +0000
Subject: [PATCH] Update summary script to read from the GERALD Summary.xml
 file instead of depending on randomly changign html code.

---
 htsworkflow/pipelines/gerald.py               |     8 +-
 htsworkflow/pipelines/summary.py              |   119 +-
 .../pipelines/test/simulate_runfolder.py      |     5 +
 .../pipelines/test/test_runfolder_rta160.py   |   277 +
 .../test/testdata/Summary-rta160.xml          | 20378 ++++++++++++++++
 5 files changed, 20771 insertions(+), 16 deletions(-)
 create mode 100644 htsworkflow/pipelines/test/test_runfolder_rta160.py
 create mode 100644 htsworkflow/pipelines/test/testdata/Summary-rta160.xml

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 980c661..35bc037 100644
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -194,8 +194,12 @@ def gerald(pathname):
     g.tree = ElementTree.parse(config_pathname).getroot()
 
     # parse Summary.htm file
-    logging.info("Parsing Summary.htm")
-    summary_pathname = os.path.join(g.pathname, 'Summary.htm')
+    summary_pathname = os.path.join(g.pathname, 'Summary.xml')
+    if os.path.exists(summary_pathname):
+        logging.info("Parsing Summary.xml")
+    else:
+        summary_pathname = os.path.join(g.pathname, 'Summary.htm')
+        logging.info("Parsing Summary.htm")
     g.summary = Summary(summary_pathname)
     # parse eland files
     g.eland_results = eland(g.pathname, g)
diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index c5db2bc..4146099 100644
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -34,6 +34,18 @@ class Summary(object):
           '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
@@ -83,10 +95,21 @@ class Summary(object):
                 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
+            self.lane_yield = int(element.find('laneYield').text)
+
+            for GeraldName, LRSName in Summary.LaneResultSummary.GERALD_TAGS.items():
+                node = element.find(GeraldName)
+                if node is None:
+                    logging.info("Couldn't find %s" % (GeraldName))
+                setattr(self, LRSName, parse_xml_mean_range(node))
+                                                                      
         def get_elements(self):
             lane_result = ElementTree.Element(
                             Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
-                            {'lane': str(self.lane), 'end': str(self.end)})
+                            {'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:
@@ -100,7 +123,7 @@ class Summary(object):
                     )
                 else:
                     element = ElementTree.SubElement(lane_result, tag)
-                    element.text = value
+                    element.text = unicode(value)
             return lane_result
 
         def set_elements(self, tree):
@@ -154,6 +177,15 @@ class Summary(object):
             data.append(self._flattened_row(r))
         return data
 
+    def _extract_lane_results(self, pathname):
+        """
+        Extract just the lane results.
+        Currently those are the only ones we care about.
+        """
+        
+        tables = self._extract_named_tables(pathname)
+
+
     def _extract_named_tables(self, pathname):
         """
         extract all the 'named' tables from a Summary.htm file
@@ -168,6 +200,48 @@ class Summary(object):
         file_body = open(pathname).read()
         file_body = file_body.replace('CHASTITY<=', 'CHASTITY&lt;=')
         tree = ElementTree.fromstring(file_body)
+
+        # are we reading the xml or the html version of the Summary file?
+        if tree.tag.lower() == 'summary':
+            # summary version
+            tables = self._extract_named_tables_from_gerald_xml(tree)
+        elif tree.tag.lower() == 'html':
+            # html version
+            tables = self._extract_named_tables_from_html(tree)
+            table_names = [ ('Lane Results Summary', 0),
+                            ('Lane Results Summary : Read 1', 0),
+                            ('Lane Results Summary : Read 2', 1),]
+            for name, end in table_names:
+                if tables.has_key(name):
+                    self._extract_lane_results_for_end(tables, name, end)
+
+        if len(self.lane_results[0])  == 0:
+            logging.warning("No Lane Results Summary Found in %s" % (pathname,))
+
+    def _extract_named_tables_from_gerald_xml(self, tree):
+        """
+        Extract useful named tables from a gerald created Summary.xml file
+        """
+        # using the function to convert to lower instead of just writing it
+        # makes the tag easier to read (IMO)
+        useful_tables = ['LaneResultsSummary'.lower(),]
+
+        tables ={}
+        for child in tree.getchildren():
+            if child.tag.lower() in  useful_tables:
+                read_tree = child.find('Read')
+                # we want 0 based.
+                read = int(read_tree.find('readNumber').text)-1
+                for element in read_tree.getchildren():
+                    if element.tag.lower() == "lane":
+                        lrs = Summary.LaneResultSummary()
+                        lrs.set_elements_from_gerald_xml(read, element)
+                        self.lane_results[lrs.end][lrs.lane] = lrs
+        # probably not useful
+        return tables
+        
+    ###### START HTML Table Extraction ########
+    def _extract_named_tables_from_html(self, tree):
         body = tree.find('body')
         tables = {}
         for i in range(len(body)):
@@ -179,17 +253,6 @@ class Summary(object):
                 tables[name] = data
         return tables
 
-    def _extract_lane_results(self, pathname):
-        tables = self._extract_named_tables(pathname)
-        table_names = [ ('Lane Results Summary', 0),
-                        ('Lane Results Summary : Read 1', 0),
-                        ('Lane Results Summary : Read 2', 1),]
-        for name, end in table_names:
-          if tables.has_key(name):
-            self._extract_lane_results_for_end(tables, name, end)
-        else:
-            logging.warning("No Lane Results Summary Found in %s" % (pathname,))
-
     def _extract_lane_results_for_end(self, tables, table_name, end):
         """
         extract the Lane Results Summary table
@@ -219,6 +282,7 @@ class Summary(object):
             lrs = Summary.LaneResultSummary(html=r)
             lrs.end = end
             self.lane_results[lrs.end][lrs.lane] = lrs
+    ###### END HTML Table Extraction ########
 
     def get_elements(self):
         summary = ElementTree.Element(Summary.SUMMARY,
@@ -248,7 +312,8 @@ class Summary(object):
         """
         Debugging function, report current object
         """
-        pass
+        tree = self.get_elements()
+        print ElementTree.tostring(tree)
 
 def tonumber(v):
     """
@@ -303,3 +368,29 @@ def parse_summary_element(element):
         return parse_mean_range_element(element)
     else:
         return element.text
+
+def parse_xml_mean_range(element):
+    """
+    Extract mean/stddev children from an element as a tuple
+    """
+    if element is None:
+        return None
+    
+    mean = element.find('mean')
+    stddev = element.find('stdev')
+    if mean is None or stddev is None:
+        raise RuntimeError("Summary.xml file format changed, expected mean/stddev tags")
+
+    return (tonumber(mean.text), tonumber(stddev.text))
+
+if __name__ == "__main__":
+    # test code
+    from optparse import OptionParser
+    parser = OptionParser('%prog [Summary.xml/Summary.htm]+')
+    opts, args = parser.parse_args()
+    if len(args) == 0:
+        parser.error('need at least one xml/html file')
+    for fname in args:
+        s = Summary(fname)
+        s.dump()
+        
diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index 555e58f..855912d 100644
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -207,6 +207,11 @@ def make_summary_ipar130_htm(gerald_dir):
     destination = os.path.join(gerald_dir, 'Summary.htm')
     shutil.copy(source, destination)
 
+def make_summary_rta160_xml(gerald_dir):
+    source = os.path.join(TESTDATA_DIR, 'Summary-rta160.xml')
+    destination = os.path.join(gerald_dir, 'Summary.xml')
+    shutil.copy(source, destination)
+
 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.
 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T
diff --git a/htsworkflow/pipelines/test/test_runfolder_rta160.py b/htsworkflow/pipelines/test/test_runfolder_rta160.py
new file mode 100644
index 0000000..d446e49
--- /dev/null
+++ b/htsworkflow/pipelines/test/test_runfolder_rta160.py
@@ -0,0 +1,277 @@
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+import unittest
+
+from htsworkflow.pipelines import eland
+from htsworkflow.pipelines import ipar
+from htsworkflow.pipelines import bustard
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.runfolder import ElementTree
+
+from htsworkflow.pipelines.test.simulate_runfolder import *
+
+
+def make_runfolder(obj=None):
+    """
+    Make a fake runfolder, attach all the directories to obj if defined
+    """
+    # make a fake runfolder directory
+    temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
+
+    runfolder_dir = os.path.join(temp_dir,
+                                 '090608_HWI-EAS229_0117_4286GAAXX')
+    os.mkdir(runfolder_dir)
+
+    data_dir = os.path.join(runfolder_dir, 'Data')
+    os.mkdir(data_dir)
+
+    intensities_dir = make_rta_intensities_1460(data_dir)
+
+    basecalls_dir = make_rta_basecalls_1460(intensities_dir)
+
+    #make_phasing_params(bustard_dir)
+    #make_bustard_config132(bustard_dir)
+
+    gerald_dir = os.path.join(basecalls_dir,
+                              'GERALD_16-06-2009_diane')
+    os.mkdir(gerald_dir)
+    make_gerald_config_100(gerald_dir)
+    make_summary_rta160_xml(gerald_dir)
+    make_eland_multi(gerald_dir, lane_list=[1,2,3,4,5,6,])
+    make_scarf(gerald_dir, lane_list=[7,])
+    make_fastq(gerald_dir, lane_list=[8,])
+
+    if obj is not None:
+        obj.temp_dir = temp_dir
+        obj.runfolder_dir = runfolder_dir
+        obj.data_dir = data_dir
+        obj.image_analysis_dir = intensities_dir
+        obj.bustard_dir = basecalls_dir
+        obj.gerald_dir = gerald_dir
+
+
+class RunfolderTests(unittest.TestCase):
+    """
+    Test components of the runfolder processing code
+    which includes firecrest, bustard, and gerald
+    """
+    def setUp(self):
+        # attaches all the directories to the object passed in
+        make_runfolder(self)
+
+    def tearDown(self):
+        shutil.rmtree(self.temp_dir)
+
+    # The only thing different from the previous RTA version is
+    # I'm processing the Summary.xml file
+
+    
+    def test_gerald(self):
+        # need to update gerald and make tests for it
+        g = gerald.gerald(self.gerald_dir)
+
+        self.failUnlessEqual(g.version,
+            '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+        self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
+        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
+        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+
+
+        # list of genomes, matches what was defined up in
+        # make_gerald_config.
+        # the first None is to offset the genomes list to be 1..9
+        # instead of pythons default 0..8
+        genomes = [None, 
+                   '/g/mm9', 
+                   '/g/mm9', 
+                   '/g/elegans190', 
+                   '/g/arabidopsis01222004',
+                   '/g/mm9', 
+                   '/g/mm9', 
+                   '/g/mm9', 
+                   '/g/mm9', ]
+
+        # test lane specific parameters from gerald config file
+        for i in range(1,9):
+            cur_lane = g.lanes[i]
+            self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
+            self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
+            self.failUnlessEqual(cur_lane.read_length, '37')
+            self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
+
+        # I want to be able to use a simple iterator
+        for l in g.lanes.values():
+          self.failUnlessEqual(l.analysis, 'eland_extended')
+          self.failUnlessEqual(l.read_length, '37')
+          self.failUnlessEqual(l.use_bases, 'Y'*37)
+
+        # test data extracted from summary file
+        clusters = [None,
+                    (281331, 11169), (203841, 13513),
+                    (220889, 15653), (137294, 14666),
+                    (129388, 14525), (262092, 10751),
+                    (185754, 13503), (233765, 9537),]
+
+        self.failUnlessEqual(len(g.summary), 1)
+        for i in range(1,9):
+            summary_lane = g.summary[0][i]
+            self.failUnlessEqual(summary_lane.cluster, clusters[i])
+            self.failUnlessEqual(summary_lane.lane, i)
+
+        xml = g.get_elements()
+        # just make sure that element tree can serialize the tree
+        xml_str = ElementTree.tostring(xml)
+        g2 = gerald.Gerald(xml=xml)
+        return
+
+        # do it all again after extracting from the xml file
+        self.failUnlessEqual(g.version, g2.version)
+        self.failUnlessEqual(g.date, g2.date)
+        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
+        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+
+        # test lane specific parameters from gerald config file
+        for i in range(1,9):
+            g_lane = g.lanes[i]
+            g2_lane = g2.lanes[i]
+            self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
+            self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
+            self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
+            self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
+
+        # test (some) summary elements
+        self.failUnlessEqual(len(g.summary), 1)
+        for i in range(1,9):
+            g_summary = g.summary[0][i]
+            g2_summary = g2.summary[0][i]
+            self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
+            self.failUnlessEqual(g_summary.lane, g2_summary.lane)
+
+            g_eland = g.eland_results
+            g2_eland = g2.eland_results
+            for lane in g_eland.results[0].keys():
+                g_results = g_eland.results[0][lane]
+                g2_results = g2_eland.results[0][lane]
+                self.failUnlessEqual(g_results.reads,
+                                     g2_results.reads)
+                if isinstance(g_results, eland.ElandLane):
+                  self.failUnlessEqual(len(g_results.mapped_reads),
+                                       len(g2_results.mapped_reads))
+                  for k in g_results.mapped_reads.keys():
+                      self.failUnlessEqual(g_results.mapped_reads[k],
+                                           g2_results.mapped_reads[k])
+
+                  self.failUnlessEqual(len(g_results.match_codes),
+                                       len(g2_results.match_codes))
+                  for k in g_results.match_codes.keys():
+                      self.failUnlessEqual(g_results.match_codes[k],
+                                           g2_results.match_codes[k])
+
+
+    def test_eland(self):
+        return
+        hg_map = {'Lambda.fa': 'Lambda.fa'}
+        for i in range(1,22):
+          short_name = 'chr%d.fa' % (i,)
+          long_name = 'hg18/chr%d.fa' % (i,)
+          hg_map[short_name] = long_name
+
+        genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
+                        5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
+        eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
+
+        # I added sequence lanes to the last 2 lanes of this test case
+        for i in range(1,7):
+            lane = eland_container.results[0][i]
+            self.failUnlessEqual(lane.reads, 6)
+            self.failUnlessEqual(lane.sample_name, "s")
+            self.failUnlessEqual(lane.lane_id, i)
+            self.failUnlessEqual(len(lane.mapped_reads), 17)
+            self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+            self.failUnlessEqual(lane.match_codes['U0'], 3)
+            self.failUnlessEqual(lane.match_codes['R0'], 2)
+            self.failUnlessEqual(lane.match_codes['U1'], 1)
+            self.failUnlessEqual(lane.match_codes['R1'], 9)
+            self.failUnlessEqual(lane.match_codes['U2'], 0)
+            self.failUnlessEqual(lane.match_codes['R2'], 12)
+            self.failUnlessEqual(lane.match_codes['NM'], 1)
+            self.failUnlessEqual(lane.match_codes['QC'], 0)
+
+        # test scarf
+        lane = eland_container.results[0][7]
+        self.failUnlessEqual(lane.reads, 5)
+        self.failUnlessEqual(lane.sample_name, 's')
+        self.failUnlessEqual(lane.lane_id, 7)
+        self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
+
+        # test fastq
+        lane = eland_container.results[0][8]
+        self.failUnlessEqual(lane.reads, 3)
+        self.failUnlessEqual(lane.sample_name, 's')
+        self.failUnlessEqual(lane.lane_id, 8)
+        self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+
+        xml = eland_container.get_elements()
+        # just make sure that element tree can serialize the tree
+        xml_str = ElementTree.tostring(xml)
+        e2 = gerald.ELAND(xml=xml)
+
+        for i in range(1,9):
+            l1 = eland_container.results[0][i]
+            l2 = e2.results[0][i]
+            self.failUnlessEqual(l1.reads, l2.reads)
+            self.failUnlessEqual(l1.sample_name, l2.sample_name)
+            self.failUnlessEqual(l1.lane_id, l2.lane_id)
+            if isinstance(l1, eland.ElandLane):
+              self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
+              self.failUnlessEqual(len(l1.mapped_reads), 17)
+              for k in l1.mapped_reads.keys():
+                  self.failUnlessEqual(l1.mapped_reads[k],
+                                       l2.mapped_reads[k])
+
+              self.failUnlessEqual(len(l1.match_codes), 9)
+              self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
+              for k in l1.match_codes.keys():
+                  self.failUnlessEqual(l1.match_codes[k],
+                                       l2.match_codes[k])
+            elif isinstance(l1, eland.SequenceLane):
+                self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
+
+    def test_runfolder(self):
+        return
+        runs = runfolder.get_runs(self.runfolder_dir)
+
+        # do we get the flowcell id from the filename?
+        self.failUnlessEqual(len(runs), 1)
+        name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+        self.failUnlessEqual(runs[0].name, name)
+
+        # do we get the flowcell id from the FlowcellId.xml file
+        make_flowcell_id(self.runfolder_dir, '207BTAAXY')
+        runs = runfolder.get_runs(self.runfolder_dir)
+        self.failUnlessEqual(len(runs), 1)
+        name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+        self.failUnlessEqual(runs[0].name, name)
+
+        r1 = runs[0]
+        xml = r1.get_elements()
+        xml_str = ElementTree.tostring(xml)
+
+        r2 = runfolder.PipelineRun(xml=xml)
+        self.failUnlessEqual(r1.name, r2.name)
+        self.failIfEqual(r2.image_analysis, None)
+        self.failIfEqual(r2.bustard, None)
+        self.failIfEqual(r2.gerald, None)
+
+
+def suite():
+    return unittest.makeSuite(RunfolderTests,'test')
+
+if __name__ == "__main__":
+    unittest.main(defaultTest="suite")
+
diff --git a/htsworkflow/pipelines/test/testdata/Summary-rta160.xml b/htsworkflow/pipelines/test/testdata/Summary-rta160.xml
new file mode 100644
index 0000000..833126b
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/Summary-rta160.xml
@@ -0,0 +1,20378 @@
+<?xml version="1.0" ?>
+<?xml-stylesheet type="text/xsl"
+	href="Summary.xsl" ?>
+
+<Summary>
+  <ChipResultsSummary>
+    <clusterCountPF>139492159</clusterCountPF>
+    <clusterCountRaw>165435470</clusterCountRaw>
+    <yield>5300699000</yield>
+  </ChipResultsSummary>
+  <ChipSummary>
+    <ChipID>Unknown</ChipID>
+    <Machine>HWI-EAS229</Machine>
+    <RunFolder>100414_HWI-EAS229_0002_6009PAAXX</RunFolder>
+  </ChipSummary>
+  <Date>Wed Apr 21 00:23:00 2010</Date>
+  <ExpandedLaneSummary>
+    <Read>
+      <readNumber>1</readNumber>
+      <Lane>
+        <laneNumber>1</laneNumber>
+        <clusterCountRaw>
+          <mean>281331.30</mean>
+          <stdev>11168.77</stdev>
+          <sumsq>12474150000.00</sumsq>
+        </clusterCountRaw>
+        <errorPF>
+          <mean>0.39</mean>
+          <stdev>0.32</stdev>
+          <sumsq>25.36</sumsq>
+        </errorPF>
+        <errorRaw>
+          <mean>0.54</mean>
+          <stdev>0.31</stdev>
+          <sumsq>38.79</sumsq>
+        </errorRaw>
+        <infoContentPF>
+          <mean>168901</mean>
+          <stdev>5058</stdev>
+          <sumsq>2855300157583</sumsq>
+        </infoContentPF>
+        <infoContentRaw>
+          <mean>184360</mean>
+          <stdev>6215</stdev>
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+          <percentUniquelyAlignedPF>69.83</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>87.95</signal20AsPctOf1>
+        </Tile>
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+          <tileNumber>0093</tileNumber>
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+          <percentUniquelyAlignedPF>69.93</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>78.12</signal20AsPctOf1>
+        </Tile>
+        <Tile>
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+          <percentUniquelyAlignedPF>70.21</percentUniquelyAlignedPF>
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+        </Tile>
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+          <oneSig>207.81</oneSig>
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+          <percentUniquelyAlignedPF>69.95</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>87.58</signal20AsPctOf1>
+        </Tile>
+        <Tile>
+          <tileNumber>0096</tileNumber>
+          <averageAlignScorePF>80.16</averageAlignScorePF>
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+          <clusterCountRaw>246187</clusterCountRaw>
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+          <percentUniquelyAlignedPF>69.85</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>80.17</signal20AsPctOf1>
+        </Tile>
+        <Tile>
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+          <averageAlignScorePF>80.03</averageAlignScorePF>
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+          <clusterCountRaw>247064</clusterCountRaw>
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+          <oneSig>216.79</oneSig>
+          <percentClustersPF>81.56</percentClustersPF>
+          <percentUniquelyAlignedPF>69.91</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>79.40</signal20AsPctOf1>
+        </Tile>
+        <Tile>
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+          <averageAlignScorePF>80.03</averageAlignScorePF>
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+          <errorPF>0.31</errorPF>
+          <oneSig>208.89</oneSig>
+          <percentClustersPF>81.54</percentClustersPF>
+          <percentUniquelyAlignedPF>69.79</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>85.74</signal20AsPctOf1>
+        </Tile>
+        <Tile>
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+          <clusterCountRaw>248235</clusterCountRaw>
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+          <percentUniquelyAlignedPF>70.05</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>79.32</signal20AsPctOf1>
+        </Tile>
+        <Tile>
+          <tileNumber>0100</tileNumber>
+          <averageAlignScorePF>78.58</averageAlignScorePF>
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+          <clusterCountRaw>249524</clusterCountRaw>
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+          <percentUniquelyAlignedPF>69.82</percentUniquelyAlignedPF>
+          <signal20AsPctOf1>78.89</signal20AsPctOf1>
+        </Tile>
+      </Read>
+    </Lane>
+  </TileResultsByLane>
+</Summary>
-- 
2.30.2