From ba05e9e5f24d2c8a9959dd1451afa79c13ade896 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Fri, 2 Oct 2009 00:15:14 +0000 Subject: [PATCH] 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. --- htsworkflow/pipelines/runfolder.py | 23 +- .../pipelines/test/simulate_runfolder.py | 82 +- .../pipelines/test/test_extract_results.py | 88 + .../test/testdata/42BRJAAXX_8_01_phasing.xml | 4 + .../test/testdata/42BRJAAXX_8_02_matrix.txt | 9 + .../test/testdata/42BRJAAXX_8_1_0039_qseq.txt | 132 + .../testdata/42BRJAAXX_BustardSummary.xml | 6989 +++++++++++++++++ .../test/testdata/s_1_0001_score.txt | 807 ++ .../pipelines/test/testdata/s_8_02_matrix.txt | 9 + 9 files changed, 8133 insertions(+), 10 deletions(-) create mode 100644 htsworkflow/pipelines/test/test_extract_results.py create mode 100644 htsworkflow/pipelines/test/testdata/42BRJAAXX_8_01_phasing.xml create mode 100644 htsworkflow/pipelines/test/testdata/42BRJAAXX_8_02_matrix.txt create mode 100644 htsworkflow/pipelines/test/testdata/42BRJAAXX_8_1_0039_qseq.txt create mode 100644 htsworkflow/pipelines/test/testdata/42BRJAAXX_BustardSummary.xml create mode 100644 htsworkflow/pipelines/test/testdata/s_1_0001_score.txt create mode 100644 htsworkflow/pipelines/test/testdata/s_8_02_matrix.txt diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index 5e9bd0b..d628f9b 100644 --- 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 8de0a7e..555e58f 100644 --- 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 /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 /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(""" @@ -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 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 index 0000000..60d4000 --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/42BRJAAXX_8_01_phasing.xml @@ -0,0 +1,4 @@ + + 0.002900 + 0.002400 + 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 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 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 index 0000000..3f6f0e3 --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/42BRJAAXX_BustardSummary.xml @@ -0,0 +1,6989 @@ + + + + + + 98964155 + 132312939 + 3661673735 + + + unknown + HWI-EAS229 + 090804_HWI-EAS229_0002_42BRJAAXX + + Thu Aug 6 20:54:28 2009 + + + + + 206925.59 + 8160.68 + 4245528089619.00 + + 1 + + 66.70 + 4.27 + 442251.82 + + 0.4700 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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 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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 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 -- 2.30.2