Test the updated version of extract results that builds srf files.

Of course this means you need illumina2srf for the code to work.
Perhaps I should add something to skip that test if its missing.

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 5e9bd0b6a544d323fbfc5feb444d1fbf671933e9..d628f9bf1623ce20f6fabec3d0206702e2197341 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -9,6 +9,7 @@ import shutil
 import stat
 import subprocess
 import sys
+import tarfile
 import time
 
 try:
@@ -386,12 +387,12 @@ def save_summary_file(gerald_object, cycle_dir):
           logging.info('Summary file %s was not found' % (summary_path,))
 
     
-def compress_score_files(gerald_object, cycle_dir):
+def compress_score_files(bustard_object, cycle_dir):
     """
     Compress score files into our result directory
     """
     # check for g.pathname/Temp a new feature of 1.1rc1
-    scores_path = gerald_object.pathname
+    scores_path = bustard_object.pathname
     scores_path_temp = os.path.join(scores_path, 'Temp')
     if os.path.isdir(scores_path_temp):
         scores_path = scores_path_temp
@@ -402,14 +403,14 @@ def compress_score_files(gerald_object, cycle_dir):
         if re.match('.*_score.txt', f):
             score_files.append(f)
 
-    tar_cmd = ['/bin/tar', 'c'] + score_files
+    tar_cmd = ['tar', 'c'] + score_files
     bzip_cmd = [ 'bzip2', '-9', '-c' ]
     tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
     tar_dest = open(tar_dest_name, 'w')
     logging.info("Compressing score files from %s" % (scores_path,))
     logging.info("Running tar: " + " ".join(tar_cmd[:10]))
     logging.info("Running bzip2: " + " ".join(bzip_cmd))
-    logging.info("Writing to %s" %(tar_dest_name))
+    logging.info("Writing to %s" %(tar_dest_name,))
 
     env = {'BZIP': '-9'}
     tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False, env=env,
@@ -417,6 +418,7 @@ def compress_score_files(gerald_object, cycle_dir):
     bzip = subprocess.Popen(bzip_cmd, stdin=tar.stdout, stdout=tar_dest)
     tar.wait()
 
+
 def compress_eland_results(gerald_object, cycle_dir):
     """
     Compress eland result files into the archive directory
@@ -444,6 +446,14 @@ def compress_eland_results(gerald_object, cycle_dir):
               bzip.wait()
     
 def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1):
+    """
+    Iterate over runfolders in runs extracting the most useful information.
+      * run parameters (in run-*.xml)
+      * eland_result files
+      * score files
+      * Summary.htm
+      * srf files (raw sequence & qualities)
+    """
     if output_base_dir is None:
         output_base_dir = os.getcwd()
 
@@ -473,14 +483,15 @@ def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1):
       save_summary_file(g, cycle_dir)
       
       # tar score files
-      compress_score_files(g, cycle_dir)
+      compress_score_files(r.bustard, cycle_dir)
 
       # compress eland result files
       compress_eland_results(g, cycle_dir)
       
       # build srf commands
       lanes = range(1,9)
-      srf_cmds = srf.make_commands(r.pathname, lanes, "woldlab", cycle_dir)
+      run_name = srf.pathname_to_run_name(r.pathname)
+      srf_cmds = srf.make_commands(run_name, lanes, site, cycle_dir)
       srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
       
 def rm_list(files, dry_run=True):

diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index 8de0a7ea831316592f6b6d64e4dfd5db6067209c..555e58f8196399c38ec644067a06e6ab3f339f7e 100644 (file)
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -8,6 +8,7 @@ import shutil
 TEST_CODE_DIR = os.path.split(__file__)[0]
 TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
 LANE_LIST = range(1,9)
+TILE_LIST = range(1,101)
 
 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
     firecrest_dir = os.path.join(data_dir, 
@@ -45,9 +46,9 @@ def make_flowcell_id(runfolder_dir, flowcell_id=None):
     f.write(config)
     f.close()
 
-def make_bustard_config132(gerald_dir):
+def make_bustard_config132(image_dir):
     source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
-    destination = os.path.join(gerald_dir, 'config.xml')
+    destination = os.path.join(image_dir, 'config.xml')
     shutil.copy(source, destination)
 
 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
@@ -76,7 +77,65 @@ def make_rta_basecalls_1460(intensities_dir):
 
     return basecalls_dir
 
+def make_qseqs(bustard_dir, in_temp=True):
+    """
+    Fill gerald directory with qseq files
+    """
+    # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
+    # was actually sequence at the start
+    source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_1_0039_qseq.txt')
+    destdir = bustard_dir
+    if not os.path.isdir(destdir):
+        os.mkdir(destdir)
+        
+    for lane in LANE_LIST:
+        for tile in TILE_LIST:
+            destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
+            shutil.copy(source, destination)
+
+    make_matrix_dir(bustard_dir)
+    make_phasing_dir(bustard_dir)
+
+    summary_source = os.path.join(TESTDATA_DIR, '42BRJAAXX_BustardSummary.xml')
+    summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
+    shutil.copy(summary_source, summary_dest)
+    
+    return destdir
+
+def make_scores(gerald_dir, in_temp=True):
+    """
+    Fill gerald directory with score temp files
+    will create the directory if it doesn't exist.
+    """
+    source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
+    destdir = gerald_dir
+    if in_temp:
+        destdir = os.path.join(destdir, 'Temp')
+    if not os.path.isdir(destdir):
+        os.mkdir(destdir)
+        
+    for lane in LANE_LIST:
+        for tile in TILE_LIST:
+            destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
+            shutil.copy(source, destination)
+            
+    return destdir
+
+def make_matrix_dir(bustard_dir):
+    """
+    Create several matrix files in <bustard_dir>/Matrix/
 
+    from pipeline 1.4    
+    """
+    destdir = os.path.join(bustard_dir, 'Matrix')
+    if not os.path.isdir(destdir):
+        os.mkdir(destdir)
+        
+    source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
+    for lane in LANE_LIST:
+        destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
+        shutil.copy(source, destination)
+        
 def make_matrix(matrix_filename):
     contents = """# Auto-generated frequency response matrix
 > A
@@ -92,8 +151,23 @@ def make_matrix(matrix_filename):
     f.write(contents)
     f.close()
 
+def make_phasing_dir(bustard_dir):
+    """
+    Create several phasing files in <bustard_dir>/Phasing/
+
+    from pipeline 1.4
+    """
+    destdir = os.path.join(bustard_dir, 'Phasing')
+    if not os.path.isdir(destdir):
+        os.mkdir(destdir)
+        
+    source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
+    for lane in LANE_LIST:
+        destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
+        shutil.copy(source, destination)
+    
 def make_phasing_params(bustard_dir):
-    for lane in range(1,9):
+    for lane in LANE_LIST:
         pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
         f = open(pathname, 'w')
         f.write("""<Parameters>
@@ -139,7 +213,7 @@ def make_eland_results(gerald_dir):
 >HWI-EAS229_24_207BTAAXX:1:7:776:582    AGCTCANCCGATCGAAAACCTCNCCAAGCAAT        NM      0       0       0
 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 """
-    for i in range(1,9):
+    for i in LANE_LIST:
         pathname = os.path.join(gerald_dir,
                                 's_%d_eland_result.txt' % (i,))
         f = open(pathname, 'w')

diff --git a/htsworkflow/pipelines/test/test_extract_results.py b/htsworkflow/pipelines/test/test_extract_results.py
new file mode 100644 (file)
index 0000000..ee0c540
--- /dev/null
+++ b/htsworkflow/pipelines/test/test_extract_results.py
@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import logging
+import os
+import tempfile
+import shutil
+import sys
+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 *
+
+logging.basicConfig(level=logging.ERROR)
+
+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)
+
+    bustard_dir = os.path.join(intensities_dir, 'Bustard1.4.0_16-06-2009_diane')
+    os.mkdir(bustard_dir)
+    make_phasing_params(bustard_dir)
+    make_bustard_config132(bustard_dir)
+    score_dir = make_scores(bustard_dir)
+    make_qseqs(bustard_dir)
+
+    gerald_dir = os.path.join(bustard_dir,
+                              'GERALD_16-06-2009_diane')
+    os.mkdir(gerald_dir)
+    make_gerald_config_100(gerald_dir)
+    make_summary_ipar130_htm(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 = bustard_dir
+        obj.gerald_dir = gerald_dir
+
+
+class RunfolderExtractTests(unittest.TestCase):
+    """
+    Test the extract result code.
+    """
+    def setUp(self):
+        # attaches all the directories to the object passed in
+        make_runfolder(self)
+
+    def tearDown(self):
+        shutil.rmtree(self.temp_dir)
+
+    def test_extract_results(self):
+        runs = runfolder.get_runs(self.runfolder_dir)
+        self.failUnlessEqual(len(runs), 1)
+        runfolder.extract_results(runs, self.temp_dir, site='asite')
+        archive = os.listdir(os.path.join(self.temp_dir, '4286GAAXX', 'C1-38'))
+        self.failUnlessEqual(len(archive), 19)
+        self.failUnless('asite_090608_HWI-EAS229_0117_4286GAAXX_6.srf' in archive)
+
+        
+def suite():
+    return unittest.makeSuite(RunfolderExtractTests,'test')
+
+if __name__ == "__main__":
+    unittest.main(defaultTest="suite")
+

diff --git a/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_01_phasing.xml b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_01_phasing.xml
new file mode 100644 (file)
index 0000000..60d4000
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_01_phasing.xml
@@ -0,0 +1,4 @@
+<Parameters>
+  <Phasing>0.002900</Phasing>
+  <Prephasing>0.002400</Prephasing>
+</Parameters>

diff --git a/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_02_matrix.txt b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_02_matrix.txt
new file mode 100644 (file)
index 0000000..23c34cb
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_02_matrix.txt
@@ -0,0 +1,9 @@
+# Auto-generated frequency response matrix
+> A
+> C
+> G
+> T
+1.31 0.14 0.00 0.00 
+0.70 0.65 0.00 0.00 
+-0.00 -0.00 1.38 0.00 
+-0.00 -0.00 0.66 0.98 

diff --git a/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_1_0039_qseq.txt b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_1_0039_qseq.txt
new file mode 100644 (file)
index 0000000..a5bace7
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_1_0039_qseq.txt
@@ -0,0 +1,132 @@
+HWI-EAS229     1       8       39      0       1717    0       1       ..........TC.TGTCAGC.TCATCTC.AATGT.CT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      5       1658    0       1       ...AATTG...A..GCCACTT.TAT..TGG.GCCTA.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      6       1653    0       1       .GTATTTTG.CGTTCTCACTTAGATTTCTAT.ACTCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      9       1713    0       1       .AAGGTCATAATACCAGTAAGGGCTCTTTCTATATCT   DHKSYYVQSGOVOVWTTVQNTXUXZ[[[[[VLVPX[[   0
+HWI-EAS229     1       8       39      9       1719    0       1       .CG..C..TG...GG..GG....AC.AA.T....CCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      9       1706    0       1       .T.AACCATTTTTCCTCGTCCCTCGTGAGGAAAAAGT   DLDEGSTMTZZZZZZZYXYZZZZZZXBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      10      1600    0       1       .CCGATGCAAATTATGATACCGCCC.CCAA.ACACCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      12      1708    0       1       ...TT..TG...GTTCGAGAT.C.CCAT.C.TGG.CC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      12      1744    0       1       .TTCCTTTC.TACACCACCACTTGTTCCCTGGCTCCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      14      1666    0       1       .AATCCTCAATGTGTGTTCGCAGGTGCGTCACAATGG   DIRSWWWYWWYYVUWQSYYWWWSMNNWTTUUVBBBBB   1
+HWI-EAS229     1       8       39      15      1660    0       1       .TCCGGTACGATGACGCAATCCACTCCAACTAGCCAG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      16      1658    0       1       .GGTTCTTTTCCTCCCC.GATCTGCGCTTTCCTCTCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      16      1675    0       1       .CAGCCAACTGTTGGACTTGTCGATCGTTCATCGCTT   DPRRWWSQUWQWWUKMFRWUWUNRUWUUWWUUUPUWW   0
+HWI-EAS229     1       8       39      16      1767    0       1       .T.TTTT.GCG.TGGTA..AGTTCCAG.C.C..CG.T   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      17      1641    0       1       .TTGTAC.ATAAGCTTAAAACATCAAGTGGACAA.AC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      17      1635    0       1       .TGGTTGAGAAAAAGCGTGATTTGTCAAATCTCTCTT   DL[[Y[WTTXSWYP[[[[ZOZZZWZZPKKX[Y[Y[YZ   1
+HWI-EAS229     1       8       39      17      1686    0       1       .TGACCAGGAGAAAGAGAGAGGAAGCAGAAGCAAGCG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      17      1627    0       1       .CCTCTCCCCATCTCATTTCTTCCCCCACCCACCCTC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      18      1618    0       1       .CTCCTCAACATCATCCGCATCTCCCCTCCGAACTAC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      18      1692    0       1       .AGGTTTTTATAGTGATCCGCTGCCGTGGTGGGCGTG   DLUWUWTSSSUMQPSGPWWWWQMUWWSWSKNPSUWUU   1
+HWI-EAS229     1       8       39      19      1776    0       1       .TTGT..GC.T.GAATATG.TTG.AGGCA.CGCGGTA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      19      1710    0       1       .GTAACTTTCGCTGCCCGGAATAGATCATTGCCAGCA   DDUGHUYYWYRFRUYWYWUHPWSWHSWQWYUYVQVBB   0
+HWI-EAS229     1       8       39      19      1726    0       1       .GA.GTTCT..CCTCT..AAT.TCGC.GCT.CGCGCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      20      1715    0       1       .ACCTCCATCCTTAGTCCCTCTGCTGCTTACGCATTC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      20      1607    0       1       .CC.C.TCCCAC..CA.CCT...GCCTCG...AAT..   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      20      1793    0       1       .CGGAGTTTTTTCTGGACAG.CCAGTTTTGGGGGGGG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      20      1601    0       1       ..CAATTTAGTTCGACCGATCTCCGGCTCTGATCGCG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      20      1720    0       1       .TTCTTTTTCGCTTTTTATCTACTTTATCTCCACCCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      21      1593    0       1       .GCTCTTCCCC.ACCCCACACCCCACACCCCCACCT.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      21      1786    0       1       .CTCCCTTGCTTCTCTACAGACAATTG.TTCACCAGG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      22      1627    0       1       .TTATATAGTTCACAGTCAGTGGTGCAGATGCCTTCT   DPXXXXXSYZZYYYZZZVYXXYXYZXXXXXXYZZZZZ   1
+HWI-EAS229     1       8       39      22      1729    0       1       .CCCCTCCCCTTTCCCCGCCCCCAACCCACCCCTGCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      22      1743    0       1       .ATCTATCTTTTTTCTTTTTCCAATACTTCTTTTGAC   DMHGYNXGZ[[XHXOXRV[X[VGOULOS[[YP[BBBB   0
+HWI-EAS229     1       8       39      23      1540    0       1       .CCATTCACATGACGTTGCCACAACAACACATTTTTC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      23      1759    0       1       .AGCCCTTCTTCCTCTACTGTGCCCACTTTCGTGGTT   DFLWUUWUWUWUWRGRGWWBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      26      1565    0       1       .CTATGACGAATCCCAAAGTCGATTTTTGCAATCGTA   DOXUXVRVXSSVYYYWSSVZZZXZZZZZZZWLWZXTB   1
+HWI-EAS229     1       8       39      27      1766    0       1       .GCCTT.AGCCTCCTCC.ACATACATGACAGCGGCTC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      27      1707    0       1       .TGGTGTTT.ATTCCAGACACAACTTGTGTAGGTGAC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      28      1555    0       1       .CAGAAATACGAATGAGATTATCAGTAATACCAAGTT   DNYYXXXX[[[ZYZ[[YXYXXY[YYXXXYWYVNQXXX   1
+HWI-EAS229     1       8       39      28      1686    0       1       .TGTTTGATGAGATTGCCCACCTGCTTTCTACCCTGA   DLTXYXYYXWMTNWYYYYXUWWWXYXXYXVNVYXYBB   1
+HWI-EAS229     1       8       39      29      1551    0       1       .ACGCGCACGCTGGACTTCAGCACGCACTTCATAGAC   DIUUUUWWVUPGQPMQUSTQPSUVMVUPUSWTWTMQU   1
+HWI-EAS229     1       8       39      29      1776    0       1       .TGTAAAAGCGAACCCATATCAGGAGTCTGC.TGCAT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      29      1673    0       1       .GTTG.ATTGG.A.GCGATCGCTATTAT.T.TGTTA.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      29      1700    0       1       .CCCCCG..TGCTT.CAGC.TGC.CCCCGTTCCC..T   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      29      1652    0       1       .TCTCCCCACTTATCAAATTCGCATTATATCTACCCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      30      1612    0       1       .GCGTAACACTCTAGTCGATTTCACTTTGAGCACTTT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      31      1842    0       1       .CCT.G..CGT.AAG.G.GAAGAGCGGCACTTTGGTG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      31      1711    0       1       .GA..C.AGGCGTC.......AT..T.G..G......   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      31      1838    0       1       .TTTGTTTC.TTA.TTGTGCTT.GCTCGCCTCGATTT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      32      1541    0       1       .AGCCGTTCGCTTAATAAATCCAATCTGCACGACCAA   DHUYZZZZZZZZYYYWUUSYZWWWVZYWYUYYUYZVB   1
+HWI-EAS229     1       8       39      32      1492    0       1       .TAATCTATT.ATATCTT.TTTTATAGTG.TGACTCT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      32      1799    0       1       .GTTAGTTTGCTCGATATACGAGGTTTTCCTCGATTT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      33      1728    0       1       .CCCCCCCCCCCCTCCCACCACCAAACTTCTTCATGC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      34      1486    0       1       .AAACTTGAGAAATTAATTTGGTAGTTGGCGTTTTTC   DDIPY[ZYWTOSVTQRQVXYZWZZMDPXSXXXYXVMU   0
+HWI-EAS229     1       8       39      35      1752    0       1       .CCTCCTCCCTCCCTCCCCCTCTCCCCCCCTC.TATT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      35      1677    0       1       .GTTCTCTCCCTCTCTCCTCTCCCTCCCCTCCCC.CC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      36      1755    0       1       .G..T.GCT.T..A.T..TG..C.TTAGTGAGGCTC.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      37      1563    0       1       .TTTAAATGTGCACTGCATTTCAAAATTTATTAAACT   DPOXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      37      1760    0       1       .CGTGTTGCCCATCTCGCAAGAGAAGGTGTCTTGCTG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   1
+HWI-EAS229     1       8       39      37      1861    0       1       .CCTTTCCCACCCTGTCTCCCCCCGCCTCTCCGCTCT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      38      1511    0       1       .AAACTGATTGGAAAACTGTTTAAATGGTTTTTTCAA   DKTXY[[W[[[YXXVVZ[[[[[YXXXYYY[[[[[[XU   1
+HWI-EAS229     1       8       39      38      1566    0       1       .ATTATATTCGCACTGCC.CTCACTC.C.AC.ACAC.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      39      1741    0       1       .TTTGCCCTTTCTAGTATGACCCAAACATATCACCGT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      41      1498    0       1       .CTGCTACATGTTGTGCTCACATGTACAAAGGCCAGT   DKVUVTGURWXXXYVTWXWTWMWWWMWRKLRXXVSWX   0
+HWI-EAS229     1       8       39      42      1842    0       1       .T.TTGCTCGCCAG..C.TATGAC.CTACC.CGGCCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      42      1690    0       1       .TCCTCTTCGTCTTTTGACTGTTTTTTTGTCTGGTAG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      43      1726    0       1       .GTATGAAAATTAGCAGAGGGTAATCACAAAATGCAA   DM[X[YULLO[[WZ[W[PY[Y[YVY[YZUPVT[[[WB   0
+HWI-EAS229     1       8       39      44      1845    0       1       .T..TG..TGA..CG...TA..ACAG.AGCCT.G.TG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      44      1850    0       1       .ACTGTTTCTTAGTTTCTCGTTCGTTCGATTACCAAC   DKYZZZZZZZXUXZZZZZZZZZZZZZZZSZZXZVVSW   1
+HWI-EAS229     1       8       39      44      1542    0       1       .TTACTTTCTTCAATTTTGTTATTCTCTTCACTCACT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      45      1539    0       1       .AAGAAGAAAAAGTCACACGGTAGTCACGTCTCATGG   DIKZYTWXZWXUZZZXSPFPNLMRXZRFQOXZVGVXZ   0
+HWI-EAS229     1       8       39      45      1450    0       1       .ATCCTCTCTCTTATCTCGCCCCCCAATCCACCACCT   DDUTHTMUVUVBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      46      1864    0       1       .ATTCGTTAGTACTAGAACCCCCCACGCTCAGCTTCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      47      1902    0       1       .TTGCCCTTTGGTGCAACAGTAGGAAGATTCAGAGCT   DPYUXYUXXYXUUXXSNTNWSGRUNRNDNXXQVGSRU   0
+HWI-EAS229     1       8       39      48      1898    0       1       .CCT.TG.A..C..ATC..C..A....TG.TC.TA..   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      49      1470    0       1       .CACCGCTCTCACATTTCGTCATCATTGCAAGCCACA   DHMGWWWWYWWWGPWYYWLOMUWYHWWWYWNWYWWBB   0
+HWI-EAS229     1       8       39      49      1593    0       1       .CCCTTGCGAACAACCATCGGCTCACCGCTATGATGT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      49      1816    0       1       .TAGCATAGTGATGCGGGTAGAACCAGCTCCACGAGA   DMLRSGRKSVUWSWXWWVWSSRGTUUWWWWVWWBBBB   0
+HWI-EAS229     1       8       39      50      1834    0       1       .AACGCTTGAAATTCTGTTTATAAAAAAAACTTTTTA   DHNVW[[YVHUVZ[[[[[[TGTTSROQQNQX[[[[XT   0
+HWI-EAS229     1       8       39      50      1612    0       1       .GTCC.AT.AA..TTGCAGTGTTCCTG.C.ACGT.T.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      51      1874    0       1       .TCCTTTTTACCTCGTCTTTTTGTCTCATCTTAATCT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      51      1772    0       1       .TGGCCTATGATGAGTATGGAGGTCAACAATCAGACA   DHVUGVYNYVMWWNYBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      52      1715    0       1       .TTATTGAGAACCGCGTCCTAGCCTTGCTAGCGCGAC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      52      1574    0       1       .A.GCTG.TCT.TGCTGA.CTGC.T.CATC..TG.GC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      52      1580    0       1       .CCTTTTTCTCGCCCCCCCCTCCGCCCGCCACCCGCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      53      1739    0       1       .CTCCTCTTCCTTCTCTTTTTCTGTTCCCTCGCACCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      53      1644    0       1       .TACAGTTTATGAAATTCCACGTGGATTCCCATTGCC   DMKUZZOXZOWZXPGTZXTGTXQFLVZXVZWGZZXXX   0
+HWI-EAS229     1       8       39      53      1679    0       1       .AAGAAAGTCACTAGATTTCGACAAGAATATAAAAAA   DKTXVPTXYYYYYWXXZ[[[Y[[XXVTUXTXSTXTQS   1
+HWI-EAS229     1       8       39      54      1800    0       1       .....CT.C...G..C..G..CA.GC..C....G..C   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      55      1456    0       1       ..AT..CC....TC.C.GCA...TTT.CG...G.C..   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      56      1449    0       1       .TCTTGTGGCTGAGTGAGCTGGGTTACCAGACGATAG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      56      1804    0       1       .AATCCTTACTATCTCGTCACGATATGGCTGCGCTCT   DMXTUVTGGGKRVXXXRXBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      57      1751    0       1       .CTTTTCGCATTGG.TGATTT.T.GCTAGA.CG.CTA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      58      1778    0       1       .TTGTTGTAATTGCCGTGTTCGTTTCACTCCCAACAG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      59      1738    0       1       .CTTTTTTT.TATTAGGTTCTATTTCGTTGAGCCCTT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      60      1557    0       1       .AGGAGGTCATCGTTGGATGATGAGGATGGTGGCGGG   DINSWUSSNSUSSUUQUWSSTSRUUQLRUWPMUUSTS   1
+HWI-EAS229     1       8       39      62      1643    0       1       .CTGTC.G.C.T.G.TT.GGCTTACGC.CTTGG.GT.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      63      1639    0       1       .TTACTGAAATCTTCACAAACATCTTAGCTGCCCTCA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      64      1459    0       1       .TACACGCCCTCCCTAACG.CGTCTCTCTCCTGCGCT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      64      1699    0       1       .CTCTTT..T.C.T..CTTGT.CGAG.CCTGACGCAG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      64      1914    0       1       .CAAATATGGCCGTACAAAGTAAACCACTTTTCAGTG   DHNQRWPWXZZXRLQQPMMQQVRTUSFSQTYBBBBBB   1
+HWI-EAS229     1       8       39      64      1881    0       1       .CTCGCCATGGATTC.GGGTCTATCTTTAGTTCT.TC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      64      1709    0       1       .T.CTCTT.CCCCTATA.AGC.ACTGT.TT..TT.TC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      65      1683    0       1       .CTATTT.G.CCA.GTCCTCACCACTCGTCTGCC.CA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      65      1780    0       1       .TTCCG.AATCG...CGGGACACC.AG.CG...CC.G   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      65      1610    0       1       .CCAGACGAAATTTTGCCTCGAACCGCAATGTCACTG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      65      1525    0       1       .CCTTTCTCTTCGTTCACCGCACGCCTCACCGCTGCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      66      1518    0       1       .CACGGCCCCAATCAATAATTTTCACATTTTCAGATA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      66      1548    0       1       .TTTTTCACTTTTTCACTATATCGAACCCAGCTTCCG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      66      1429    0       1       .TTTTTCATAATTAGCTAATACGTCTCCCACAACGGT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      67      1726    0       1       .AGTACTTCAAATCCTGAAATTGATGTTCGGAGTTAC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      67      1738    0       1       .TACTACAACTACAACTACCACCACAACAACTGTTGC   DNZZXXXXYZZZYWSZZZZYXYZZZWYXYWYZYWYZZ   1
+HWI-EAS229     1       8       39      68      1925    0       1       .TGG.TCGGGGCGGGGGC.TACCGATGGGGGTAGAAG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      69      1746    0       1       .TTCTCGCGAGGACTGGCTCAATCAGCTGGGAATAGA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      69      1713    0       1       .GTCTG.C..GGTTCTCGGGCGAGGGGCGTCTGGGCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      70      1749    0       1       .GC...A.T.T.C..TCGCATTGATCGCAAC.ACGCG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      70      1816    0       1       .G.G..TTG......G....ATCC.TA.AA...GC.G   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      72      1768    0       1       .GTT.TC.A.TGC.GTTGTGTGCTGATCAG.GTT..G   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      72      1958    0       1       ..G..T...T..T...G..CC...A.T...GCATC..   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      72      1576    0       1       .GGCGCGCGAAACGTGTGCTATATCGTTGACCGGAGA   DDPQWWWWUTPSWWUWPPGNLMTVWUUUUUWTQSPSB   0
+HWI-EAS229     1       8       39      73      1771    0       1       .GCTTTCTACTT.CCCCC.CACCTCACCC.CCCCCCC   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      74      1688    0       1       .TTTC.TGT.CGCTCGCTTCGACATGAT.TCTACG.G   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      74      1595    0       1       .GCTTTTCTTT.G.C.CTGCGCCAGCACACTCATCCG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      74      1515    0       1       .CCTTT.A.A...T..CG...G.T.CAG.GTC.T.TG   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      75      1590    0       1       .TTGGGATACGTTTACTCTTTTTTTTGTTAAATGTTT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      75      1911    0       1       .AATTTTAATTTTGGTAGGCAGACGTAGGTTCGTAGA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      78      1544    0       1       ..CCCCT.G.C..G.GCTG.CCCCC.T.GC..C.ACT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      78      1774    0       1       .C...C.TTC.CCCCCC.CG.GCTCGACA..CAC.C.   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      78      1646    0       1       .CTGTGGTTGTTATGCGAT.TCGACTTTCGACTCTTT   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      79      1792    0       1       .CCGCTGTAGCACCAACTAGCACCAATTTAGCACCGA   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB   0
+HWI-EAS229     1       8       39      80      1795    0       1       .GTGTAATTATGATATTCGCCTTTCTAGAAGCAAATT   DOZPYOY[Z[Y[[[[[[[ZY[[Y[[WYZZLOR[Z[[Z   1
+HWI-EAS229     1       8       39      80      1800    0       1       .ACAGATCAGACAAATCCTCCTCCTTCGTAGACGGCT   DMYUWPWYUYYWWWWYWYWYWYYWWYYYVNWWWYWWW   1

diff --git a/htsworkflow/pipelines/test/testdata/42BRJAAXX_BustardSummary.xml b/htsworkflow/pipelines/test/testdata/42BRJAAXX_BustardSummary.xml
new file mode 100644 (file)
index 0000000..3f6f0e3
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/42BRJAAXX_BustardSummary.xml
@@ -0,0 +1,6989 @@
+<?xml version="1.0" ?>
+<?xml-stylesheet type="text/xsl"
+       href="BustardSummary.xsl" ?>
+
+<BustardSummary>
+  <ChipResultsSummary>
+    <clusterCountPF>98964155</clusterCountPF>
+    <clusterCountRaw>132312939</clusterCountRaw>
+    <yield>3661673735</yield>
+  </ChipResultsSummary>
+  <ChipSummary>
+    <ChipID>unknown</ChipID>
+    <Machine>HWI-EAS229</Machine>
+    <RunFolder>090804_HWI-EAS229_0002_42BRJAAXX</RunFolder>
+  </ChipSummary>
+  <Date>Thu Aug  6 20:54:28 2009</Date>
+  <ExpandedLaneSummary>
+    <Read>
+      <Lane>
+        <clusterCountRaw>
+          <mean>206925.59</mean>
+          <stdev>8160.68</stdev>
+          <sumsq>4245528089619.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>1</laneNumber>
+        <percentClustersPF>
+          <mean>66.70</mean>
+          <stdev>4.27</stdev>
+          <sumsq>442251.82</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.4700</phasingApplied>
+        <prephasingApplied>0.2800</prephasingApplied>
+        <signalAverage1to3>
+          <mean>107.24</mean>
+          <stdev>13.10</stdev>
+          <sumsq>1155409.00</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>103.50</mean>
+          <stdev>13.57</stdev>
+          <sumsq>1078616.22</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>0.79</mean>
+          <stdev>2.58</stdev>
+          <sumsq>714.89</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>2.11</mean>
+          <stdev>0.54</stdev>
+          <sumsq>471.03</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>133925.04</mean>
+          <stdev>7031.74</stdev>
+          <sumsq>1798486729842.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>2</laneNumber>
+        <percentClustersPF>
+          <mean>84.51</mean>
+          <stdev>1.82</stdev>
+          <sumsq>714464.67</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.4700</phasingApplied>
+        <prephasingApplied>0.2800</prephasingApplied>
+        <signalAverage1to3>
+          <mean>134.23</mean>
+          <stdev>6.99</stdev>
+          <sumsq>1806537.23</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>131.36</mean>
+          <stdev>7.79</stdev>
+          <sumsq>1731628.77</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>1.15</mean>
+          <stdev>0.63</stdev>
+          <sumsq>171.91</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>1.99</mean>
+          <stdev>0.67</stdev>
+          <sumsq>440.91</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>215053.98</mean>
+          <stdev>7120.49</stdev>
+          <sumsq>4629840873462.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>3</laneNumber>
+        <percentClustersPF>
+          <mean>64.44</mean>
+          <stdev>4.12</stdev>
+          <sumsq>416920.07</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.4700</phasingApplied>
+        <prephasingApplied>0.2800</prephasingApplied>
+        <signalAverage1to3>
+          <mean>102.20</mean>
+          <stdev>9.31</stdev>
+          <sumsq>1052999.51</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>95.13</mean>
+          <stdev>8.59</stdev>
+          <sumsq>912227.07</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>1.25</mean>
+          <stdev>0.56</stdev>
+          <sumsq>188.01</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>2.52</mean>
+          <stdev>0.72</stdev>
+          <sumsq>687.97</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>206047.96</mean>
+          <stdev>4146.85</stdev>
+          <sumsq>4247278625182.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>4</laneNumber>
+        <percentClustersPF>
+          <mean>63.67</mean>
+          <stdev>1.98</stdev>
+          <sumsq>405721.90</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.4700</phasingApplied>
+        <prephasingApplied>0.2800</prephasingApplied>
+        <signalAverage1to3>
+          <mean>145.40</mean>
+          <stdev>10.06</stdev>
+          <sumsq>2124184.04</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>134.97</mean>
+          <stdev>10.89</stdev>
+          <sumsq>1833548.77</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>1.14</mean>
+          <stdev>0.63</stdev>
+          <sumsq>169.40</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>2.23</mean>
+          <stdev>0.71</stdev>
+          <sumsq>548.58</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>86445.94</mean>
+          <stdev>4123.73</stdev>
+          <sumsq>748973563210.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>5</laneNumber>
+        <percentClustersPF>
+          <mean>86.65</mean>
+          <stdev>1.39</stdev>
+          <sumsq>751080.81</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.4700</phasingApplied>
+        <prephasingApplied>0.2800</prephasingApplied>
+        <signalAverage1to3>
+          <mean>98.74</mean>
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+          <signal20AsPctOf1>81.04</signal20AsPctOf1>
+          <tileNumber>0076</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129389</clusterCountPF>
+          <clusterCountRaw>153025</clusterCountRaw>
+          <oneSig>143.95</oneSig>
+          <percentClustersPF>84.55</percentClustersPF>
+          <signal20AsPctOf1>79.37</signal20AsPctOf1>
+          <tileNumber>0077</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>128645</clusterCountPF>
+          <clusterCountRaw>153555</clusterCountRaw>
+          <oneSig>144.50</oneSig>
+          <percentClustersPF>83.78</percentClustersPF>
+          <signal20AsPctOf1>76.80</signal20AsPctOf1>
+          <tileNumber>0078</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129149</clusterCountPF>
+          <clusterCountRaw>153805</clusterCountRaw>
+          <oneSig>150.10</oneSig>
+          <percentClustersPF>83.97</percentClustersPF>
+          <signal20AsPctOf1>71.67</signal20AsPctOf1>
+          <tileNumber>0079</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>128955</clusterCountPF>
+          <clusterCountRaw>152843</clusterCountRaw>
+          <oneSig>146.00</oneSig>
+          <percentClustersPF>84.37</percentClustersPF>
+          <signal20AsPctOf1>73.25</signal20AsPctOf1>
+          <tileNumber>0080</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>128630</clusterCountPF>
+          <clusterCountRaw>152788</clusterCountRaw>
+          <oneSig>152.62</oneSig>
+          <percentClustersPF>84.19</percentClustersPF>
+          <signal20AsPctOf1>82.19</signal20AsPctOf1>
+          <tileNumber>0081</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129098</clusterCountPF>
+          <clusterCountRaw>152096</clusterCountRaw>
+          <oneSig>151.03</oneSig>
+          <percentClustersPF>84.88</percentClustersPF>
+          <signal20AsPctOf1>78.48</signal20AsPctOf1>
+          <tileNumber>0082</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129170</clusterCountPF>
+          <clusterCountRaw>152339</clusterCountRaw>
+          <oneSig>150.02</oneSig>
+          <percentClustersPF>84.79</percentClustersPF>
+          <signal20AsPctOf1>68.09</signal20AsPctOf1>
+          <tileNumber>0083</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>128646</clusterCountPF>
+          <clusterCountRaw>151901</clusterCountRaw>
+          <oneSig>154.00</oneSig>
+          <percentClustersPF>84.69</percentClustersPF>
+          <signal20AsPctOf1>72.92</signal20AsPctOf1>
+          <tileNumber>0084</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129009</clusterCountPF>
+          <clusterCountRaw>152733</clusterCountRaw>
+          <oneSig>153.72</oneSig>
+          <percentClustersPF>84.47</percentClustersPF>
+          <signal20AsPctOf1>67.12</signal20AsPctOf1>
+          <tileNumber>0085</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>128824</clusterCountPF>
+          <clusterCountRaw>153183</clusterCountRaw>
+          <oneSig>153.68</oneSig>
+          <percentClustersPF>84.10</percentClustersPF>
+          <signal20AsPctOf1>72.02</signal20AsPctOf1>
+          <tileNumber>0086</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>128212</clusterCountPF>
+          <clusterCountRaw>153721</clusterCountRaw>
+          <oneSig>157.47</oneSig>
+          <percentClustersPF>83.41</percentClustersPF>
+          <signal20AsPctOf1>76.79</signal20AsPctOf1>
+          <tileNumber>0087</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129372</clusterCountPF>
+          <clusterCountRaw>153851</clusterCountRaw>
+          <oneSig>151.75</oneSig>
+          <percentClustersPF>84.09</percentClustersPF>
+          <signal20AsPctOf1>84.88</signal20AsPctOf1>
+          <tileNumber>0088</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129972</clusterCountPF>
+          <clusterCountRaw>153959</clusterCountRaw>
+          <oneSig>153.48</oneSig>
+          <percentClustersPF>84.42</percentClustersPF>
+          <signal20AsPctOf1>78.01</signal20AsPctOf1>
+          <tileNumber>0089</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>130203</clusterCountPF>
+          <clusterCountRaw>154770</clusterCountRaw>
+          <oneSig>159.43</oneSig>
+          <percentClustersPF>84.13</percentClustersPF>
+          <signal20AsPctOf1>75.52</signal20AsPctOf1>
+          <tileNumber>0090</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>130310</clusterCountPF>
+          <clusterCountRaw>155233</clusterCountRaw>
+          <oneSig>155.45</oneSig>
+          <percentClustersPF>83.94</percentClustersPF>
+          <signal20AsPctOf1>73.08</signal20AsPctOf1>
+          <tileNumber>0091</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>131031</clusterCountPF>
+          <clusterCountRaw>155793</clusterCountRaw>
+          <oneSig>159.22</oneSig>
+          <percentClustersPF>84.11</percentClustersPF>
+          <signal20AsPctOf1>78.51</signal20AsPctOf1>
+          <tileNumber>0092</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>129988</clusterCountPF>
+          <clusterCountRaw>154952</clusterCountRaw>
+          <oneSig>123.83</oneSig>
+          <percentClustersPF>83.89</percentClustersPF>
+          <signal20AsPctOf1>97.40</signal20AsPctOf1>
+          <tileNumber>0093</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>121980</clusterCountPF>
+          <clusterCountRaw>157271</clusterCountRaw>
+          <oneSig>157.75</oneSig>
+          <percentClustersPF>77.56</percentClustersPF>
+          <signal20AsPctOf1>79.43</signal20AsPctOf1>
+          <tileNumber>0094</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>130910</clusterCountPF>
+          <clusterCountRaw>158146</clusterCountRaw>
+          <oneSig>157.60</oneSig>
+          <percentClustersPF>82.78</percentClustersPF>
+          <signal20AsPctOf1>77.25</signal20AsPctOf1>
+          <tileNumber>0095</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>132939</clusterCountPF>
+          <clusterCountRaw>158613</clusterCountRaw>
+          <oneSig>160.28</oneSig>
+          <percentClustersPF>83.81</percentClustersPF>
+          <signal20AsPctOf1>79.96</signal20AsPctOf1>
+          <tileNumber>0096</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>132820</clusterCountPF>
+          <clusterCountRaw>158963</clusterCountRaw>
+          <oneSig>165.88</oneSig>
+          <percentClustersPF>83.55</percentClustersPF>
+          <signal20AsPctOf1>64.64</signal20AsPctOf1>
+          <tileNumber>0097</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>133454</clusterCountPF>
+          <clusterCountRaw>159639</clusterCountRaw>
+          <oneSig>169.43</oneSig>
+          <percentClustersPF>83.60</percentClustersPF>
+          <signal20AsPctOf1>64.90</signal20AsPctOf1>
+          <tileNumber>0098</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>133260</clusterCountPF>
+          <clusterCountRaw>160753</clusterCountRaw>
+          <oneSig>169.35</oneSig>
+          <percentClustersPF>82.90</percentClustersPF>
+          <signal20AsPctOf1>71.95</signal20AsPctOf1>
+          <tileNumber>0099</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>134518</clusterCountPF>
+          <clusterCountRaw>161902</clusterCountRaw>
+          <oneSig>171.62</oneSig>
+          <percentClustersPF>83.09</percentClustersPF>
+          <signal20AsPctOf1>72.47</signal20AsPctOf1>
+          <tileNumber>0100</tileNumber>
+        </Tile>
+        <readNumber>1</readNumber>
+      </Read>
+      <laneNumber>8</laneNumber>
+    </Lane>
+  </TileResultsByLane>
+</BustardSummary>

diff --git a/htsworkflow/pipelines/test/testdata/s_1_0001_score.txt b/htsworkflow/pipelines/test/testdata/s_1_0001_score.txt
new file mode 100644 (file)
index 0000000..c811071
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/s_1_0001_score.txt
@@ -0,0 +1,807 @@
+# Lane 1 : Tile 1 : Raw : Read 1
+4685939 bases of sequence found
+55933 were errors
+8532 were blanks
+ 1.20 percent error rate
+ 0.18 percent blank rate
+
+unique alignments : 126647 (total score 15145668)
+cycles : 37
+
+Breakdown of errors by cycle
+Cycle: Err pc: Blank pc:
+1       0.87    0.17
+2       1.60    0.08
+3       1.56    0.06
+4       1.38    0.06
+5       1.36    0.07
+6       1.48    0.06
+7       0.98    0.06
+8       0.92    0.06
+9       1.01    0.06
+10      1.03    0.07
+11      1.02    0.06
+12      0.89    0.06
+13      0.88    0.07
+14      0.84    0.05
+15      0.91    0.08
+16      0.87    0.06
+17      0.96    0.05
+18      0.94    0.06
+19      1.04    0.06
+20      0.95    0.07
+21      0.90    0.07
+22      0.86    0.07
+23      0.99    0.13
+24      0.96    0.08
+25      0.96    0.08
+26      0.99    0.09
+27      1.03    0.18
+28      1.08    0.18
+29      1.07    0.26
+30      1.16    0.33
+31      1.28    0.40
+32      1.25    0.44
+33      1.64    0.54
+34      2.03    0.58
+35      2.00    0.64
+36      2.14    0.67
+37      2.45    0.61
+
+Error rate relative to reference base (including blanks)
+(Given a reference base, what is it sequenced as?)
+
+Really:        Read As:
+       N pc    A pc    C pc    G pc    T pc
+A       0.18   97.92    1.25    0.39    0.26
+C       0.18    0.23   98.95    0.23    0.41
+G       0.18    0.29    0.27   98.80    0.47
+T       0.19    0.17    0.51    0.23   98.89
+
+Error rate relative to reference base (excluding blanks)
+(Given a reference base, what is it sequenced as?)
+
+Really:        Read As:
+       A pc    C pc    G pc    T pc
+A      98.09    1.25    0.39    0.26
+C       0.23   99.13    0.23    0.41
+G       0.30    0.27   98.97    0.47
+T       0.17    0.51    0.23   99.08
+
+Error rate relative to sequenced base (excluding ref blanks)
+(Given a sequenced base, what was it really?)
+
+Read As:       Really:
+       A pc    C pc    G pc    T pc
+N      26.16   24.03   23.42   26.39
+A      99.34    0.22    0.28    0.17
+C       1.35   97.86    0.26    0.52
+G       0.42    0.23   99.12    0.24
+T       0.28    0.40    0.46   98.87
+
+Breakdown of errors by nucleotide
+Read As:       Really:
+       A ct    C ct    G ct    T ct
+N      2232    2050    1998    2252
+A      1212263 2648    3363    2039
+C      15505   1122933 3028    6007
+G      4789    2561    1127774 2713
+T      3268    4651    5361    1158477
+
+
+Full breakdown of errors by cycle and nucleotide
+Cycle: Read As:        Really:
+               A ct    C ct    G ct    T ct
+1      N       71      39      54      50
+1      A       43465   56      120     66
+1      C       218     26692   40      80
+1      G       127     55      30058   33
+1      T       87      129     92      25115
+2      N       37      14      29      23
+2      A       42361   37      101     58
+2      C       1165    21533   73      159
+2      G       113     36      33301   58
+2      T       58      65      100     27326
+3      N       16      26      15      16
+3      A       33739   44      75      56
+3      C       1037    30720   97      230
+3      G       104     25      27687   47
+3      T       76      98      85      32454
+4      N       25      19      20      15
+4      A       30345   31      66      53
+4      C       894     31174   102     178
+4      G       116     29      33502   45
+4      T       79      88      67      29799
+5      N       28      21      20      22
+5      A       33797   35      72      39
+5      C       911     28790   77      206
+5      G       113     29      31399   55
+5      T       66      65      59      30843
+6      N       20      20      17      19
+6      A       33160   29      83      34
+6      C       1079    31888   103     209
+6      G       103     29      31820   35
+6      T       53      60      59      27827
+7      N       19      28      12      23
+7      A       32652   45      76      52
+7      C       430     30112   52      174
+7      G       105     30      30067   56
+7      T       68      77      75      32494
+8      N       22      18      19      17
+8      A       31797   43      86      42
+8      C       366     30009   65      159
+8      G       119     44      31022   62
+8      T       45      76      60      32576
+9      N       23      20      18      18
+9      A       31177   45      74      39
+9      C       468     31812   68      210
+9      G       111     27      30382   53
+9      T       54      67      61      31920
+10     N       23      15      21      26
+10     A       33538   45      76      53
+10     C       540     31637   69      166
+10     G       94      31      30435   37
+10     T       42      85      67      29647
+11     N       18      24      21      19
+11     A       32806   36      69      42
+11     C       493     31165   72      179
+11     G       101     26      31285   60
+11     T       51      82      74      30024
+12     N       19      20      24      19
+12     A       31974   34      76      36
+12     C       394     31650   70      132
+12     G       101     31      30855   43
+12     T       56      73      76      30964
+13     N       21      23      22      19
+13     A       32914   43      80      50
+13     C       313     30538   55      144
+13     G       90      34      30189   41
+13     T       63      76      120     31812
+14     N       18      21      15      14
+14     A       32945   45      69      33
+14     C       275     30682   60      137
+14     G       109     35      30134   37
+14     T       62      100     98      31758
+15     N       26      27      29      25
+15     A       32344   43      64      57
+15     C       329     31087   63      152
+15     G       115     29      30187   49
+15     T       71      83      95      31772
+16     N       18      14      20      19
+16     A       32614   52      73      36
+16     C       270     30913   66      105
+16     G       98      46      30058   39
+16     T       68      97      147     31894
+17     N       18      18      17      9
+17     A       32326   46      72      45
+17     C       343     30336   88      174
+17     G       91      50      30262   40
+17     T       62      88      117     32445
+18     N       24      16      13      18
+18     A       32009   46      89      46
+18     C       309     31234   66      152
+18     G       90      44      30280   41
+18     T       62      112     130     31866
+19     N       24      18      10      21
+19     A       31978   31      83      38
+19     C       541     30946   69      151
+19     G       91      22      30591   45
+19     T       57      103     81      31747
+20     N       25      20      17      21
+20     A       32248   38      71      42
+20     C       359     30888   87      134
+20     G       103     30      30297   51
+20     T       63      105     120     31928
+21     N       21      23      23      16
+21     A       32187   68      68      39
+21     C       222     31121   66      122
+21     G       101     57      30279   46
+21     T       78      129     142     31839
+22     N       23      21      24      18
+22     A       32377   53      62      37
+22     C       244     31011   64      123
+22     G       118     42      30392   49
+22     T       78      86      131     31694
+23     N       35      41      38      45
+23     A       32161   46      73      47
+23     C       352     30770   65      158
+23     G       91      45      30185   53
+23     T       75      118     133     32116
+24     N       27      24      27      22
+24     A       31942   61      69      35
+24     C       235     31056   76      160
+24     G       100     67      30020   55
+24     T       78      122     163     32308
+25     N       25      26      21      35
+25     A       32196   59      99      48
+25     C       254     30607   69      160
+25     G       89      45      30383   62
+25     T       72      117     141     32139
+26     N       27      34      34      25
+26     A       32311   49      71      35
+26     C       340     30453   70      150
+26     G       113     44      30371   64
+26     T       81      110     125     32140
+27     N       61      48      64      55
+27     A       31843   49      86      56
+27     C       294     30725   74      158
+27     G       128     55      30388   74
+27     T       85      122     122     32160
+28     N       72      49      50      59
+28     A       31897   71      89      41
+28     C       257     30705   79      126
+28     G       128     74      30361   81
+28     T       96      138     181     32093
+29     N       85      83      74      90
+29     A       32231   73      63      45
+29     C       259     30448   79      121
+29     G       138     83      30203   88
+29     T       102     142     161     32079
+30     N       108     97      95      123
+30     A       31826   102     75      47
+30     C       223     30650   87      155
+30     G       123     103     30269   92
+30     T       86      148     218     32020
+31     N       140     121     101     145
+31     A       31705   113     96      52
+31     C       221     30503   94      161
+31     G       143     107     30476   107
+31     T       117     177     224     31844
+32     N       148     137     133     142
+32     A       32084   128     76      50
+32     C       215     30236   94      164
+32     G       150     118     30292   112
+32     T       112     184     179     31893
+33     N       188     147     160     191
+33     A       31353   150     134     86
+33     C       272     30280   118     191
+33     G       215     120     30432   129
+33     T       156     220     281     31821
+34     N       189     175     174     198
+34     A       31795   188     148     94
+34     C       274     30016   127     157
+34     G       260     217     30039   138
+34     T       195     298     460     31499
+35     N       196     199     192     224
+35     A       31483   201     179     130
+35     C       309     29892   111     202
+35     G       217     223     30127   195
+35     T       175     273     305     31808
+36     N       208     214     210     217
+36     A       31091   189     181     140
+36     C       396     30610   116     226
+36     G       265     230     29924   219
+36     T       205     251     268     31481
+37     N       184     190     165     234
+37     A       31592   224     219     140
+37     C       404     30044   197     242
+37     G       316     249     29822   222
+37     T       234     287     344     31332
+
+Error rate relative to reference by cycle/nucleotide
+Cycle: Read As:        Really:
+               A prp   C prp   G prp   T prp
+@1     N        0.002   0.001   0.002   0.002
+@1     A        0.989   0.002   0.004   0.003
+@1     C        0.005   0.990   0.001   0.003
+@1     G        0.003   0.002   0.990   0.001
+@1     T        0.002   0.005   0.003   0.991
+@2     N        0.001   0.001   0.001   0.001
+@2     A        0.969   0.002   0.003   0.002
+@2     C        0.027   0.993   0.002   0.006
+@2     G        0.003   0.002   0.991   0.002
+@2     T        0.001   0.003   0.003   0.989
+@3     N        0.000   0.001   0.001   0.000
+@3     A        0.965   0.001   0.003   0.002
+@3     C        0.030   0.994   0.003   0.007
+@3     G        0.003   0.001   0.990   0.001
+@3     T        0.002   0.003   0.003   0.989
+@4     N        0.001   0.001   0.001   0.000
+@4     A        0.965   0.001   0.002   0.002
+@4     C        0.028   0.995   0.003   0.006
+@4     G        0.004   0.001   0.992   0.001
+@4     T        0.003   0.003   0.002   0.990
+@5     N        0.001   0.001   0.001   0.001
+@5     A        0.968   0.001   0.002   0.001
+@5     C        0.026   0.995   0.002   0.007
+@5     G        0.003   0.001   0.993   0.002
+@5     T        0.002   0.002   0.002   0.990
+@6     N        0.001   0.001   0.001   0.001
+@6     A        0.964   0.001   0.003   0.001
+@6     C        0.031   0.996   0.003   0.007
+@6     G        0.003   0.001   0.992   0.001
+@6     T        0.002   0.002   0.002   0.989
+@7     N        0.001   0.001   0.000   0.001
+@7     A        0.981   0.001   0.003   0.002
+@7     C        0.013   0.994   0.002   0.005
+@7     G        0.003   0.001   0.993   0.002
+@7     T        0.002   0.003   0.002   0.991
+@8     N        0.001   0.001   0.001   0.001
+@8     A        0.983   0.001   0.003   0.001
+@8     C        0.011   0.994   0.002   0.005
+@8     G        0.004   0.001   0.993   0.002
+@8     T        0.001   0.003   0.002   0.991
+@9     N        0.001   0.001   0.001   0.001
+@9     A        0.979   0.001   0.002   0.001
+@9     C        0.015   0.995   0.002   0.007
+@9     G        0.003   0.001   0.993   0.002
+@9     T        0.002   0.002   0.002   0.990
+@10    N        0.001   0.000   0.001   0.001
+@10    A        0.980   0.001   0.002   0.002
+@10    C        0.016   0.994   0.002   0.006
+@10    G        0.003   0.001   0.992   0.001
+@10    T        0.001   0.003   0.002   0.991
+@11    N        0.001   0.001   0.001   0.001
+@11    A        0.980   0.001   0.002   0.001
+@11    C        0.015   0.995   0.002   0.006
+@11    G        0.003   0.001   0.993   0.002
+@11    T        0.002   0.003   0.002   0.990
+@12    N        0.001   0.001   0.001   0.001
+@12    A        0.982   0.001   0.002   0.001
+@12    C        0.012   0.995   0.002   0.004
+@12    G        0.003   0.001   0.992   0.001
+@12    T        0.002   0.002   0.002   0.993
+@13    N        0.001   0.001   0.001   0.001
+@13    A        0.985   0.001   0.003   0.002
+@13    C        0.009   0.994   0.002   0.004
+@13    G        0.003   0.001   0.991   0.001
+@13    T        0.002   0.002   0.004   0.992
+@14    N        0.001   0.001   0.000   0.000
+@14    A        0.986   0.001   0.002   0.001
+@14    C        0.008   0.993   0.002   0.004
+@14    G        0.003   0.001   0.992   0.001
+@14    T        0.002   0.003   0.003   0.993
+@15    N        0.001   0.001   0.001   0.001
+@15    A        0.984   0.001   0.002   0.002
+@15    C        0.010   0.994   0.002   0.005
+@15    G        0.003   0.001   0.992   0.002
+@15    T        0.002   0.003   0.003   0.991
+@16    N        0.001   0.000   0.001   0.001
+@16    A        0.986   0.002   0.002   0.001
+@16    C        0.008   0.993   0.002   0.003
+@16    G        0.003   0.001   0.990   0.001
+@16    T        0.002   0.003   0.005   0.994
+@17    N        0.001   0.001   0.001   0.000
+@17    A        0.984   0.002   0.002   0.001
+@17    C        0.010   0.993   0.003   0.005
+@17    G        0.003   0.002   0.990   0.001
+@17    T        0.002   0.003   0.004   0.992
+@18    N        0.001   0.001   0.000   0.001
+@18    A        0.985   0.001   0.003   0.001
+@18    C        0.010   0.993   0.002   0.005
+@18    G        0.003   0.001   0.990   0.001
+@18    T        0.002   0.004   0.004   0.992
+@19    N        0.001   0.001   0.000   0.001
+@19    A        0.978   0.001   0.003   0.001
+@19    C        0.017   0.994   0.002   0.005
+@19    G        0.003   0.001   0.992   0.001
+@19    T        0.002   0.003   0.003   0.992
+@20    N        0.001   0.001   0.001   0.001
+@20    A        0.983   0.001   0.002   0.001
+@20    C        0.011   0.994   0.003   0.004
+@20    G        0.003   0.001   0.990   0.002
+@20    T        0.002   0.003   0.004   0.992
+@21    N        0.001   0.001   0.001   0.000
+@21    A        0.987   0.002   0.002   0.001
+@21    C        0.007   0.991   0.002   0.004
+@21    G        0.003   0.002   0.990   0.001
+@21    T        0.002   0.004   0.005   0.993
+@22    N        0.001   0.001   0.001   0.001
+@22    A        0.986   0.002   0.002   0.001
+@22    C        0.007   0.994   0.002   0.004
+@22    G        0.004   0.001   0.991   0.002
+@22    T        0.002   0.003   0.004   0.993
+@23    N        0.001   0.001   0.001   0.001
+@23    A        0.983   0.001   0.002   0.001
+@23    C        0.011   0.992   0.002   0.005
+@23    G        0.003   0.001   0.990   0.002
+@23    T        0.002   0.004   0.004   0.991
+@24    N        0.001   0.001   0.001   0.001
+@24    A        0.986   0.002   0.002   0.001
+@24    C        0.007   0.991   0.003   0.005
+@24    G        0.003   0.002   0.989   0.002
+@24    T        0.002   0.004   0.005   0.992
+@25    N        0.001   0.001   0.001   0.001
+@25    A        0.987   0.002   0.003   0.001
+@25    C        0.008   0.992   0.002   0.005
+@25    G        0.003   0.001   0.989   0.002
+@25    T        0.002   0.004   0.005   0.991
+@26    N        0.001   0.001   0.001   0.001
+@26    A        0.983   0.002   0.002   0.001
+@26    C        0.010   0.992   0.002   0.005
+@26    G        0.003   0.001   0.990   0.002
+@26    T        0.002   0.004   0.004   0.992
+@27    N        0.002   0.002   0.002   0.002
+@27    A        0.982   0.002   0.003   0.002
+@27    C        0.009   0.991   0.002   0.005
+@27    G        0.004   0.002   0.989   0.002
+@27    T        0.003   0.004   0.004   0.989
+@28    N        0.002   0.002   0.002   0.002
+@28    A        0.983   0.002   0.003   0.001
+@28    C        0.008   0.989   0.003   0.004
+@28    G        0.004   0.002   0.987   0.002
+@28    T        0.003   0.004   0.006   0.991
+@29    N        0.003   0.003   0.002   0.003
+@29    A        0.982   0.002   0.002   0.001
+@29    C        0.008   0.988   0.003   0.004
+@29    G        0.004   0.003   0.988   0.003
+@29    T        0.003   0.005   0.005   0.989
+@30    N        0.003   0.003   0.003   0.004
+@30    A        0.983   0.003   0.002   0.001
+@30    C        0.007   0.986   0.003   0.005
+@30    G        0.004   0.003   0.985   0.003
+@30    T        0.003   0.005   0.007   0.987
+@31    N        0.004   0.004   0.003   0.004
+@31    A        0.981   0.004   0.003   0.002
+@31    C        0.007   0.983   0.003   0.005
+@31    G        0.004   0.003   0.983   0.003
+@31    T        0.004   0.006   0.007   0.986
+@32    N        0.005   0.004   0.004   0.004
+@32    A        0.981   0.004   0.002   0.002
+@32    C        0.007   0.982   0.003   0.005
+@32    G        0.005   0.004   0.984   0.003
+@32    T        0.003   0.006   0.006   0.986
+@33    N        0.006   0.005   0.005   0.006
+@33    A        0.974   0.005   0.004   0.003
+@33    C        0.008   0.979   0.004   0.006
+@33    G        0.007   0.004   0.978   0.004
+@33    T        0.005   0.007   0.009   0.982
+@34    N        0.006   0.006   0.006   0.006
+@34    A        0.972   0.006   0.005   0.003
+@34    C        0.008   0.972   0.004   0.005
+@34    G        0.008   0.007   0.971   0.004
+@34    T        0.006   0.010   0.015   0.982
+@35    N        0.006   0.006   0.006   0.007
+@35    A        0.972   0.007   0.006   0.004
+@35    C        0.010   0.971   0.004   0.006
+@35    G        0.007   0.007   0.975   0.006
+@35    T        0.005   0.009   0.010   0.977
+@36    N        0.006   0.007   0.007   0.007
+@36    A        0.967   0.006   0.006   0.004
+@36    C        0.012   0.972   0.004   0.007
+@36    G        0.008   0.007   0.975   0.007
+@36    T        0.006   0.008   0.009   0.975
+@37    N        0.006   0.006   0.005   0.007
+@37    A        0.965   0.007   0.007   0.004
+@37    C        0.012   0.969   0.006   0.008
+@37    G        0.010   0.008   0.970   0.007
+@37    T        0.007   0.009   0.011   0.974
+
+Information Content By Cycle
+       Bases this cycle                Bases so far
+Cycle: Equiv info:     Align:  Total:  Equiv info:     Align:  Total:
+~1     121135.20       126433  221956  121135.20       126433  221956
+~2     118981.66       126544  220204  240116.88       252977  442160
+~3     118709.06       126574  219216  358825.94       379551  661376
+~4     119387.88       126568  218313  478213.81       506119  879689
+~5     119571.18       126556  217983  597785.00       632675  1097672
+~6     119189.21       126571  217603  716974.19       759246  1315275
+~7     120874.08       126565  217439  837848.25       885811  1532714
+~8     121116.88       126571  217155  958965.12       1012382 1749869
+~9     120779.02       126568  216903  1079744.12      1138950 1966772
+~10    120721.09       126562  217060  1200465.25      1265512 2183832
+~11    120762.78       126565  217584  1321228.00      1392077 2401416
+~12    121319.63       126565  217610  1442547.62      1518642 2619026
+~13    121292.62       126562  217564  1563840.25      1645204 2836590
+~14    121490.08       126579  217562  1685330.38      1771783 3054152
+~15    121105.89       126540  217267  1806436.25      1898323 3271419
+~16    121309.71       126576  216955  1927746.00      2024899 3488374
+~17    120892.80       126585  216878  2048638.75      2151484 3705252
+~18    120964.48       126576  216864  2169603.25      2278060 3922116
+~19    120717.50       126574  216842  2290320.75      2404634 4138958
+~20    120936.81       126564  216644  2411257.50      2531198 4355602
+~21    121079.27       126564  216639  2532336.75      2657762 4572241
+~22    121315.66       126561  216490  2653652.50      2784323 4788731
+~23    120625.85       126488  216289  2774278.25      2910811 5005020
+~24    120734.09       126547  216482  2895012.25      3037358 5221502
+~25    120758.35       126540  216381  3015770.50      3163898 5437883
+~26    120670.38       126527  216482  3136441.00      3290425 5654365
+~27    120291.03       126419  216156  3256732.00      3416844 5870521
+~28    120022.73       126417  216128  3376754.75      3543261 6086649
+~29    119949.20       126315  215933  3496704.00      3669576 6302582
+~30    119421.66       126224  215800  3616125.75      3795800 6518382
+~31    118718.27       126140  215620  3734844.00      3921940 6734002
+~32    118778.77       126087  215509  3853622.75      4048027 6949511
+~33    116782.13       125958  215248  3970405.00      4173985 7164759
+~34    115034.91       125905  215123  4085440.00      4299890 7379882
+~35    114996.52       125830  214997  4200436.50      4425720 7594879
+~36    114382.40       125792  214951  4314819.00      4551512 7809830
+~37    113076.75       125868  215037  4427896.00      4677380 8024867
+
+The 30 most common words with 2 blanks or less:
+Ranking        Occurrences     Words
+1      411     GTTGTGTTGTGTTGTGTTGTGTTGTGTTGTGTTGTGT 
+2      382     TGTGTTGTGTTGTGTTGTGTTGTGTTGTGTTGTGTTG 
+3      324     TGTTGTGTTGTGTTGTGTTGTGTTGTGTTGTGTTGTG 
+4      271     GTGTTGTGTTGTGTTGTGTTGTGTTGTGTTGTGTTGT 
+5      239     GTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGT 
+6      234     AACACAACACAACACAACACAACACAACACAACACAA 
+7      214     ACAACACAACACAACACAACACAACACAACACAACAC 
+8      209     CACAACACAACACAACACAACACAACACAACACAACA 
+9      206     AAGACAAGACAAGACAAGACAAGACAAGACAAGACAA 
+10     203     AGACAAGACAAGACAAGACAAGACAAGACAAGACAAG CAAGACAAGACAAGACAAGACAAGACAAGACAAGACA 
+11     201     CAACACAACACAACACAACACAACACAACACAACACA 
+12     200     ACACAACACAACACAACACAACACAACACAACACAAC 
+13     170     ACAAGACAAGACAAGACAAGACAAGACAAGACAAGAC 
+14     152     TGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTG 
+15     149     AGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 
+16     142     AGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAG 
+17     135     CTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCT 
+18     118     AAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAA 
+19     117     GACAAGACAAGACAAGACAAGACAAGACAAGACAAGA 
+20     103     TTGTGTTGTGTTGTGTTGTGTTGTGTTGTGTTGTGTT 
+21     102     GAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGA 
+22     100     GAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGA 
+23     80      TTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT TTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTT 
+24     76      TCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTCTTGTC 
+25     53      CTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCT 
+26     47      CTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCT 
+27     42      TCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTC 
+28     37      TCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTC 
+29     36      GTCATGTCTTGTCATGTCTTGTCATGTCTTGTCATGT 
+30     35      CATGTCTTGTCATGTCTTGTCATGTCTTGTCATGTCT 
+
+The 30 most common blank patterns (N=any nonblank character)
+Ranking        Occurrences     Words
+1      209206  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 
+2      2010    N.................................... 
+3      1020    NN................................... 
+4      727     NNN.................................. 
+5      472     NNNN................................. 
+6      441     ..................................... 
+7      422     NNNNN................................ 
+8      376     .NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 
+9      206     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN....... 
+10     191     .NNNNNNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNN 
+11     181     NNNNNNNN..NNNNN...................... 
+12     180     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.N 
+13     162     NNNNNNNNNNNNNNNNNNNNNNNNNNNN......... 
+14     160     N.NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...... 
+15     158     NNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNNN 
+16     157     NNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNN 
+17     153     NNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNN 
+18     152     NNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNN 
+19     150     NNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.... 
+20     148     NNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNN 
+21     146     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNN 
+22     145     NNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNN 
+23     144     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN. 
+24     143     NNNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNNNN 
+25     142     NNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 
+26     141     NNNNNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNN 
+27     140     NNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNNN 
+28     139     NNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNN 
+29     137     NNNNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNN 
+30     136     NNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNN 
+
+Log likelihood scores
+Cycle: Read As:        Really:
+               A       C       G       T 
+>1     N       -30     -65     -47     -51
+>1     A       225     -289    -256    -282
+>1     C       -208    189     -282    -252
+>1     G       -237    -273    214     -296
+>1     T       -246    -229    -243    191
+>2     N       -25     -80     -40     -54
+>2     A       233     -306    -262    -286
+>2     C       -127    118     -249    -215
+>2     G       -247    -296    220     -276
+>2     T       -267    -262    -243    208
+>3     N       -55     -25     -58     -55
+>3     A       228     -288    -265    -278
+>3     C       -147    135     -251    -214
+>3     G       -242    -304    219     -277
+>3     T       -263    -252    -258    209
+>4     N       -33     -49     -46     -63
+>4     A       230     -299    -266    -275
+>4     C       -154    142     -249    -225
+>4     G       -246    -306    224     -287
+>4     T       -257    -253    -265    210
+>5     N       -35     -52     -55     -49
+>5     A       236     -298    -267    -293
+>5     C       -150    138     -258    -216
+>5     G       -244    -303    220     -275
+>5     T       -267    -267    -272    221
+>6     N       -44     -44     -54     -47
+>6     A       235     -305    -260    -299
+>6     C       -147    136     -250    -219
+>6     G       -249    -304    227     -296
+>6     T       -272    -266    -267    220
+>7     N       -52     -28     -76     -40
+>7     A       227     -286    -263    -279
+>7     C       -184    166     -277    -224
+>7     G       -245    -300    219     -273
+>7     T       -268    -262    -263    216
+>8     N       -38     -50     -47     -54
+>8     A       226     -287    -256    -288
+>8     C       -191    170     -267    -228
+>8     G       -241    -285    213     -270
+>8     T       -286    -263    -273    225
+>9     N       -38     -46     -53     -53
+>9     A       229     -284    -262    -290
+>9     C       -183    162     -267    -218
+>9     G       -243    -305    220     -276
+>9     T       -277    -267    -272    224
+>10    N       -43     -66     -48     -35
+>10    A       228     -287    -264    -280
+>10    C       -177    161     -267    -228
+>10    G       -251    -299    227     -291
+>10    T       -285    -254    -264    218
+>11    N       -55     -38     -46     -52
+>11    A       234     -296    -267    -289
+>11    C       -180    162     -264    -224
+>11    G       -249    -308    222     -271
+>11    T       -277    -256    -261    216
+>12    N       -52     -49     -38     -52
+>12    A       234     -297    -262    -294
+>12    C       -190    172     -266    -238
+>12    G       -248    -299    224     -285
+>12    T       -274    -262    -261    217
+>13    N       -48     -43     -45     -54
+>13    A       227     -288    -261    -282
+>13    C       -199    177     -275    -233
+>13    G       -252    -295    226     -286
+>13    T       -270    -262    -242    208
+>14    N       -44     -34     -54     -58
+>14    A       235     -286    -267    -300
+>14    C       -205    181     -271    -235
+>14    G       -244    -293    222     -291
+>14    T       -271    -250    -251    208
+>15    N       -49     -47     -42     -51
+>15    A       229     -287    -270    -275
+>15    C       -197    175     -269    -231
+>15    G       -242    -301    219     -279
+>15    T       -265    -258    -252    210
+>16    N       -46     -60     -40     -43
+>16    A       230     -279    -265    -295
+>16    C       -206    184     -267    -247
+>16    G       -248    -281    221     -288
+>16    T       -267    -251    -233    200
+>17    N       -38     -38     -42     -77
+>17    A       229     -284    -265    -285
+>17    C       -195    170     -254    -224
+>17    G       -252    -278    222     -288
+>17    T       -272    -256    -244    208
+>18    N       -29     -53     -64     -46
+>18    A       224     -284    -255    -284
+>18    C       -200    177     -268    -231
+>18    G       -252    -283    223     -287
+>18    T       -271    -245    -239    202
+>19    N       -30     -48     -79     -39
+>19    A       232     -301    -258    -292
+>19    C       -176    160     -266    -232
+>19    G       -252    -314    228     -283
+>19    T       -274    -249    -259    211
+>20    N       -36     -49     -58     -47
+>20    A       232     -293    -265    -288
+>20    C       -193    172     -255    -236
+>20    G       -246    -300    221     -277
+>20    T       -270    -248    -242    204
+>21    N       -47     -41     -41     -62
+>21    A       226     -267    -267    -291
+>21    C       -214    188     -267    -241
+>21    G       -247    -272    217     -282
+>21    T       -261    -239    -235    196
+>22    N       -43     -49     -41     -57
+>22    A       232     -278    -271    -294
+>22    C       -210    185     -269    -240
+>22    G       -241    -286    216     -279
+>22    T       -261    -256    -238    203
+>23    N       -54     -45     -50     -40
+>23    A       228     -284    -264    -283
+>23    C       -194    172     -268    -229
+>23    G       -252    -282    220     -275
+>23    T       -263    -243    -238    199
+>24    N       -43     -50     -43     -54
+>24    A       228     -272    -266    -296
+>24    C       -212    181     -261    -229
+>24    G       -247    -265    213     -273
+>24    T       -262    -242    -229    194
+>25    N       -51     -49     -61     -31
+>25    A       219     -273    -251    -282
+>25    C       -208    180     -265    -228
+>25    G       -253    -283    219     -269
+>25    T       -265    -244    -236    198
+>26    N       -53     -40     -40     -57
+>26    A       231     -282    -265    -296
+>26    C       -195    173     -264    -231
+>26    G       -243    -284    213     -267
+>26    T       -260    -246    -241    200
+>27    N       -43     -57     -40     -49
+>27    A       222     -281    -256    -275
+>27    C       -202    176     -262    -229
+>27    G       -237    -274    207     -261
+>27    T       -258    -242    -242    199
+>28    N       -34     -56     -55     -46
+>28    A       220     -265    -255    -289
+>28    C       -208    182     -259    -239
+>28    G       -237    -261    203     -257
+>28    T       -252    -237    -225    188
+>29    N       -46     -47     -54     -42
+>29    A       225     -264    -271    -285
+>29    C       -207    182     -259    -240
+>29    G       -234    -256    199     -253
+>29    T       -250    -235    -230    189
+>30    N       -46     -52     -53     -38
+>30    A       215     -249    -262    -283
+>30    C       -214    181     -255    -230
+>30    G       -239    -247    197     -252
+>30    T       -257    -233    -217    185
+>31    N       -41     -50     -60     -39
+>31    A       208     -245    -252    -278
+>31    C       -214    180     -251    -228
+>31    G       -233    -245    193     -245
+>31    T       -244    -225    -215    178
+>32    N       -44     -48     -50     -46
+>32    A       210     -240    -262    -281
+>32    C       -215    180     -251    -227
+>32    G       -230    -241    190     -243
+>32    T       -245    -224    -225    182
+>33    N       -42     -56     -51     -41
+>33    A       192     -232    -237    -256
+>33    C       -205    171     -241    -220
+>33    G       -215    -240    181     -237
+>33    T       -231    -216    -205    168
+>34    N       -46     -50     -50     -43
+>34    A       186     -223    -233    -253
+>34    C       -204    173     -237    -228
+>34    G       -206    -214    168     -234
+>34    T       -221    -203    -184    151
+>35    N       -49     -48     -50     -41
+>35    A       179     -219    -224    -238
+>35    C       -199    168     -243    -217
+>35    G       -214    -213    167     -219
+>35    T       -226    -207    -202    162
+>36    N       -48     -47     -48     -46
+>36    A       178     -222    -223    -235
+>36    C       -189    161     -243    -213
+>36    G       -205    -212    162     -214
+>36    T       -219    -210    -207    163
+>37    N       -50     -48     -56     -36
+>37    A       173     -215    -216    -235
+>37    C       -187    155     -219    -210
+>37    G       -198    -208    157     -213
+>37    T       -213    -204    -196    155
+
+Cumulative errors by cycle
+Cycle: 1       2       3       4       5
+!1     125330  126433  126433  126433  126433
+!2     123478  126485  126544  126544  126544
+!3     121621  126432  126574  126574  126574
+!4     119966  126327  126568  126568  126568
+!5     118395  126151  126556  126556  126556
+!6     116747  125952  126571  126571  126571
+!7     115677  125775  126565  126565  126565
+!8     114666  125627  126571  126571  126571
+!9     113563  125445  126568  126568  126568
+!10    112449  125247  126562  126562  126562
+!11    111387  125030  126565  126565  126565
+!12    110462  124835  126565  126565  126565
+!13    109545  124634  126562  126562  126562
+!14    108713  124442  126579  126579  126579
+!15    107751  124171  126540  126540  126540
+!16    106931  123971  126576  126576  126576
+!17    106010  123696  126585  126585  126585
+!18    105106  123393  126576  126576  126576
+!19    104133  123046  126574  126574  126574
+!20    103248  122711  126564  126564  126564
+!21    102436  122390  126564  126564  126564
+!22    101656  122077  126561  126561  126561
+!23    100677  121658  126488  126488  126488
+!24    99884   121345  126547  126547  126547
+!25    99045   120962  126540  126540  126540
+!26    98191   120538  126527  126527  126527
+!27    97267   119962  126419  126419  126419
+!28    96397   119475  126417  126417  126417
+!29    95473   118877  126315  126315  126315
+!30    94545   118189  126224  126224  126224
+!31    93562   117440  126140  126140  126140
+!32    92682   116663  126087  126087  126087
+!33    91764   115889  125385  125958  125958
+!34    90677   115109  124668  125814  125905
+!35    89710   114249  123991  125563  125801
+!36    88756   113426  123311  125289  125699
+!37    87838   112643  122629  125025  125655
+
+
+

diff --git a/htsworkflow/pipelines/test/testdata/s_8_02_matrix.txt b/htsworkflow/pipelines/test/testdata/s_8_02_matrix.txt
new file mode 100644 (file)
index 0000000..23c34cb
--- /dev/null
+++ b/htsworkflow/pipelines/test/testdata/s_8_02_matrix.txt
@@ -0,0 +1,9 @@
+# Auto-generated frequency response matrix
+> A
+> C
+> G
+> T
+1.31 0.14 0.00 0.00 
+0.70 0.65 0.00 0.00 
+-0.00 -0.00 1.38 0.00 
+-0.00 -0.00 0.66 0.98