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Commit message:
Upload ctat tools. |
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ctat_rsem_align_and_estimate_abundance.xml ctat_trinity_tool_wrapper.py test-data/Sp.Trinity.fasta test-data/Sp_hs.left.fq test-data/Sp_hs.right.fq test-data/reads.left.simPE.fq test-data/reads.right.simPE.fq test-data/reads.simPE.Trinity.fasta |
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| diff -r 000000000000 -r 8605f8570c77 ctat_rsem_align_and_estimate_abundance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_rsem_align_and_estimate_abundance.xml Tue Jul 17 11:48:59 2018 -0400 |
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| @@ -0,0 +1,165 @@ +<tool id="ctat_rsem_align_and_estimate_abundance" name="ctat_rsem_align_and_estimate_abundance" version="1.0.0" profile="17.05"> + + <description>run RSEM to estimate transcript abundances</description> + + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package">subprocess32</requirement> + <requirement type="package">bzip2</requirement> + <requirement type="package" version="1.3.0">rsem</requirement> + <requirement type="package" version="3">bioconductor-edger</requirement> + <requirement type="package" version="2">bioconductor-qvalue</requirement> + <requirement type="package" version="2.6.6">trinity</requirement> + </requirements> + + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/ctat_trinity_tool_wrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference --output_dir "subdir" + + ## Inputs. + #if str($inputs.paired_or_single) == "paired": + --left $inputs.left_input --right $inputs.right_input + #if $inputs.left_input.ext == 'fa': + --seqType fa + #else: + --seqType fq + #end if + #if str($inputs.library_type) != "None": + --SS_lib_type $inputs.library_type + #end if + + #else: + --single $inputs.input + #if str($inputs.input.ext) == 'fa': + --seqType fa + #else: + --seqType fq + #end if + #if str($inputs.library_type) != "None": + --SS_lib_type $inputs.library_type + #end if + #end if + ]]> + + </command> + <inputs> + <param format="fasta" name="transcripts" type="data" label="Transcripts Fasta" help="Fasta sequences against which reads are aligned. This may be the Assembled Transcripts file from Trinity." /> + + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <when value="paired"> + <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="FR">FR</option> + <option value="RF">RF</option> + </param> + + </when> + <when value="single"> + <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="F">F</option> + <option value="R">R</option> + </param> + + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="subdir/RSEM.isoforms.results"/> + <data format="txt" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="subdir/RSEM.genes.results"/> + </outputs> + + <tests> + <test> + <param name="transcripts" value="reads.simPE.Trinity.fasta" /> + <param name="paired_or_single" value="paired" /> + <param name="left_input" value="reads.left.simPE.fq" /> + <param name="right_input" value="reads.right.simPE.fq" /> + <param name="library_type" value="None" /> + + <output name="transcript_counts" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> + </assert_contents> + </output> + + <output name="gene_counts" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> + </assert_contents> + </output> + </test> + <test> + <param name="transcripts" value="Sp.Trinity.fasta" /> + <param name="paired_or_single" value="paired" /> + <param name="left_input" value="Sp_ds.left.fq" /> + <param name="right_input" value="Sp_ds.right.fq" /> + <param name="library_type" value="None" /> + + <output name="transcript_counts" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> + </assert_contents> + </output> + + <output name="gene_counts" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> + </assert_contents> + </output> + </test> + <test> + <param name="transcripts" value="Sp.Trinity.fasta" /> + <param name="paired_or_single" value="paired" /> + <param name="left_input" value="Sp_hs.left.fq" /> + <param name="right_input" value="Sp_hs.right.fq" /> + <param name="library_type" value="None" /> + + <output name="transcript_counts" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> + </assert_contents> + </output> + + <output name="gene_counts" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> + </assert_contents> + </output> + </test> + </tests> + + <help> +.. class:: infomark + +Use RSEM to generate transcript quantification for genes and isoforms. + +To learn more about RSEM read their paper_ or visit their website_. + +If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ . + +.. _paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323 +.. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html +.. _website: http://deweylab.biostat.wisc.edu/rsem/README.html +.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki + </help> + + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 8605f8570c77 ctat_trinity_tool_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_trinity_tool_wrapper.py Tue Jul 17 11:48:59 2018 -0400 |
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| @@ -0,0 +1,123 @@ +#!/usr/bin/env python + + +# borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools. + +""" +Wrapper that execute a program and its arguments but reports standard error +messages only if the program exit status was not 0 +Example: ./stderr_wrapper.py myprog arg1 -f arg2 +""" + +import sys, subprocess, os +print sys.version + +assert sys.version_info[:2] >= ( 2, 4 ) + +TRINITY_BASE_DIR = "" +if os.environ.has_key('TRINITY_HOME'): + TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; +elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions. + # 2017-09-26 + # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility. + # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. + # I just found distutils.spawn.find_executable() which might work, but already implemented the below. + try: + pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) + except: + msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0]) + sys.stderr.write(msg) + # t, v, tb = sys.exc_info() + # raise t, v, tb + # For some reason the above was giving a syntax error. + # A simple raise should reraise the existing exception. + raise + else: + TrinityPath, err_info = pipe1.communicate() + # FIX - probably should be checking err_info for errors... + # Determine the TRINITY_BASE_DIR from output1. + # If TrinityPath is a link, we need to dereference the link. + TrinityPath = TrinityPath.rstrip() # Need to strip off a newline. + # print "Trinity that was found is: {:s}".format(repr(TrinityPath)) + # print os.path.islink(TrinityPath) + TrinityPath = os.path.abspath(TrinityPath) + # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath) + # print msg + # print os.path.islink(TrinityPath) + while os.path.islink(TrinityPath): + # print "That path is a link." + TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) + # print "The new path is: {:s}".format(TrinityPath) + # Take off the last part of the path (which is the Trinity command) + TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) +else: + sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.") + sys.exit(1) + + +# get bindir +bindir = sys.argv[0] +bindir = bindir.split("/") +if len(bindir) > 1: + bindir.pop() + bindir = "/".join(bindir) +else: + bindir = "." + + +## add locations of tools to path setting. +#TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt"; +#for line in open(TOOL_PATHS_FILE): +# line = line.rstrip() +# os.environ['PATH'] += ":" + line + +# Add TrinityPath and its utils to the PATH environment variable. +# print "Initially the PATH env variable is:\n\t{:s}".format(os.environ['PATH']) +os.environ['PATH'] = os.environ['PATH'] + ":{:s}:{:s}".format(TRINITY_BASE_DIR,TRINITY_BASE_DIR+"/util") +# print "Now the PATH env variable is:\n\t{:s}".format(os.environ['PATH']) + + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + # Get command-line arguments + args = sys.argv + # Remove name of calling program, i.e. ./stderr_wrapper.py + args.pop(0) + # If there are no arguments left, we're done + if len(args) == 0: + return + + # If one needs to silence stdout + #args.append( ">" ) + #args.append( "/dev/null" ) + print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR) + print "The PATH env variable is:\n\t{:s}".format(os.environ['PATH']) + + args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); + + cmdline = " ".join(args) + + print "The command being invoked is:\n\t{:s}".format(cmdline) + + + try: + # Run program + err_capture = open("stderr.txt", 'w') + proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) + returncode = proc.wait() + err_capture.close() + + + if returncode != 0: + raise Exception + + except Exception: + # Running Grinder failed: write error message to stderr + err_text = open("stderr.txt").readlines() + stop_err( "ERROR:\n" + "\n".join(err_text)) + + +if __name__ == "__main__": __main__() |
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| diff -r 000000000000 -r 8605f8570c77 test-data/Sp.Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp.Trinity.fasta Tue Jul 17 11:48:59 2018 -0400 |
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| b'@@ -0,0 +1,5256 @@\n+>TRINITY_DN75_c0_g1_i1 len=570 path=[548:0-569] [-1, 548, -2]\n+AAGGTTTAAGCAAAGTCCCGTTGCTAGCAATATGCCTACTTATGGAAGCTCTAACCGTAC\n+GGTTCAATCCCAAAAGCGCTCGATTCGGGACAAATATATACAAATGCCAAATGATTCTAC\n+GCAAGCTTCCCTTATGCCTTCTTATACCAGAAAAACTAGCAATGCATCAAAGAAACTTAC\n+TACTGAAGAAGATGAATTTTATGACTCAGAAGAAGAGCCTGAAGCCATAGTTCACAGGGA\n+TACATCGGCGTTAGAGAGAACTGTACTCAATTTTATAAACAGCAGTACTGCTAAGGAACT\n+CTCTGATACTGCTAGTTGCCCTTTGTCCCACTCGAAACTCCTTTTAGAGCATCGTCCTTT\n+CCAGACACTTGCCGAAGCTTGTATCATCAAACATCCTGATGACGTTCCTAGCAAACCTGG\n+TAGACGTGGAAGGCGTCGTGAAAAAAATCCTATGGGCCAAAAAATCGTCAATGCTTGTAT\n+GGAAACCATGGAAGGATATTATGCAATTGATAATCTAATTGCCAAATGCGAGTTTCTTGG\n+TAATCGTATATCTAAAGGTATGGCCTCGTG\n+>TRINITY_DN55_c0_g1_i1 len=2583 path=[2561:0-393 5289:394-417 2956:418-1586 5290:1587-1610 4149:1611-1646 5292:1647-1670 4209:1671-2169 5291:2170-2193 4732:2194-2582] [-1, 2561, 5289, 2956, 5290, 4149, 5292, 4209, 5291, 4732, -2]\n+GTTATTTATAACCCATTTCCCACTAAGTTCCTTTGTTGAACGCTTAAAAGATTGTTCATA\n+CGTTTGAACATATTTAAAATCACGTTATAGCTGAGAAGAAAACCCCTTTTCAAGTAATAA\n+AAGTATATTTAATTACTTATTTTACCCTTTATATTACGAACTGTACGACTTAACCGGTTT\n+TATCTATAAATTCCTTCATTTTTCTTTGTTTTCGTTTTCAATTTGATTTCATTACAAAAT\n+GTCGAACACAGAAACTTTCAAGTTTGAGGCTGAAATCAGCCAGTTGATGTCTTTAATCAT\n+CAACACTGTTTATTCTAACAAGGAAATTTTCCTTCGTGAGCTTATTTCCAACGCTTCCGA\n+TGCCTTGGACAAAATTCGTTATCAAAGCCTTTCCGATCCTCATGCCTTAGACGCTGAGAA\n+GGATCTTTTCATTCGCATTACTCCTGACAAGGAGAACAAAATCCTTAGCATTCGCGATAC\n+CGGTATTGGTATGACCAAGAATGACCTTATCAACAACCTTGGTGTTATCGCCAAGTCTGG\n+TACTAAGCAGTTTATGGAAGCTGCTGCTTCTGGTGCTGATATCTCCATGATTGGTCAATT\n+CGGTGTTGGTTTCTACTCTGCATACTTGGTTGCCGACAAGGTCCAAGTCGTAAGTAAGCA\n+TAATGACGATGAGCAATACATCTGGGAATCCTCTGCTGGTGGTAGCTTCACCGTCACTTT\n+GGACACCGATGGACCTCGCTTGTTACGTGGTACCGAGATTCGTCTCTTCATGAAAGAAGA\n+CCAACTTCAATACCTCGAGGAAAAGACTATCAAAGATACCGTCAAGAAACATAGTGAGTT\n+CATCTCTTACCCCATTCAATTAGTTGTTACCCGTGAGGTTGAGAAGGAGGTCCCTGAAGA\n+AGAAGAGACCGAAGAAGTTAAGAATGAAGAAGACGATAAGGCTCCTAAGATTGAGGAGGT\n+TGATGATGAATCTGAGAAGAAGGAGAAGAAGACCAAGAAGGTCAAGGAGACCACCACTGA\n+GACTGAGGAGTTGAACAAGACCAAGCCCATTTGGACTCGCAACCCCAGTGAAGTTACCAA\n+GGAAGAGTATGCCTCTTTCTACAAGTCTTTGACTAACGACTGGGAAGACCATTTGGCCGT\n+CAAGCACTTCAGCGTTGAAGGTCAATTGGAATTCCGTGCCATTCTTTTCGTCCCCCGCCG\n+CGCTCCTATGGACCTTTTTGAGGCCAAGCGTAAGAAGAACAACATCAAGCTCTATGTTCG\n+CCGTGTTTTCATTACCGACGACTGTGAAGAGTTGATTCCTGAATGGTTGGGTTTCATTAA\n+GGGTGTTGTTGATTCTGAGGACTTGCCCTTGAACTTGTCTCGTGAGATGCTTCAACAAAA\n+CAAGATCATGAAGGTTATTCGTAAGAACCTTGTCCGTCGTTGTCTTGATATGTTCAACGA\n+GATTGCCGAGGACAAGGAGAACTTCAAGACTTTCTACGATGCTTTCAGCAAGAATTTGAA\n+GCTTGGTATCCATGAGGATGCTGCTAACCGCCCTGCTTTAGCCAAGCTTTTGCGTTACAA\n+CTCCCTTAACTCCCCTGATGATCTTATCAGTCTTGAGGACTACATCACTAAGATGCCCGA\n+ACATCAAAAGAACATTTATTTCATCACTGGTGAATCTAAGCAAGCCGTTGAGAACTCTCC\n+CTTCTTGGAAATCTTCCGTGCCAAGAAGTTTGATGTTCTCTTCATGGTTGACCCCATTGA\n+TGAGTACGCTGTCACTCAACTCAAGGAATTCGAGGGCAAGAAATTGGTTAACATTACTAA\n+GGATGGTCTTGAGTTGGAAGAGACTGACGAGGAGAAGGCTGCTCGCGAGAAGCTCGAAAA\n+AGAGTATGAGGAGTTTGCTAAGCAACTTAAGACCATTTTGGGTGACAAGGTTGAAAAGGT\n+TGTTGTTTCTAACAAGATTGTTGGTTCTCCTTGCTTGTTAACTACCGGTCAATATGGTTG\n+GTCTGCTAACATGGAACGTATCATGAAGGCTCAAGCCCTTCGTGATACTTCTATGAGTGC\n+CTATATGTCTAGCCGCAAGACTTTTGAGATTAACCCCAAGTCTCCCATCATTGCTGAGCT\n+CAAGAAGAAGGTTGAGGAGAATGGTGCCGAAGACCGCTCTGTGAAGGATCTTGCTACTAT\n+TTTGTATGAGACCGCCTTGTTGTCCTCTGGTTTCACTCTTGATGACCCTAGTGCTTATGC\n+TCAACGTATCAACCGTCTTATTTCTCTTGGTCTTAGCATTGACGAAGAGGAGGAGGCTCC\n+TATTGAGGAAATTTCTACCGAATCCGTCGCTGCTGAAAACAATGCTGAGAGCAAGATGGA\n+GGAAGTCGATTAAATCAAATGCATCTAATGTGTCTTTCCAAAATTTATGCATATAATGTT\n+TTTCTTGGATTAAAGCAAGTTATCCTATACATTGTTAACGATTCTAGTGTCTGTTGTCAT\n+TCAAAAATTTCTTTCTACACGATTTTTCTTAATACACACTAGATTACAGGTTGTTTGGAA\n+GTTGTTATAATATGGAATGTTGATTAGTAATATTAAAGTTTATGGATACTTATTAGTACA\n+TCA\n+>TRINITY_DN72_c0_g1_i1 len=381 path=[551:0-380] [-1, 551, -2]\n+TTCCAGTCCTGTCTTATGAGAACCGTACTTTGAATTCTGAAGTCCATTTCTTAAAATTTG\n+TTTTACCGGTGAAGACGGTAAACTCAAATCAGGATTACTAACGACCCTTTGCTTTTTATG\n+CAGTCGTTTAGACACGGTCTGTCCTGGCGAGCGCTTTTGCTTGTTTAACTCTGAAACTGT\n+CACGTCTAAAAAGTTCCAAACTTCCGATTCCGAAGAAATTCTCTTCAAACCATTATCTTT\n+TTCCTTACATTTTCCTCTTTTCATTTCAAGGTTTCTTCAATCCGCCTGGCTTGACATCGA\n+TTCTTTACAAAAATGGAGGAACACGGTCGTACCAACTCACAATGTAGCTTG'..b'GCTTTCCAATGGATTGAACG\n+AATTGCTTGACAGTCTCCTTGGGACTCTCAGTGCTACCACTGTATACAAAAAGGTCGATA\n+ACACCACCGATCATTCGATACTGAAGATAATCTTGGCGCAAAAGAACATCCATTCCATTA\n+GCTGTAAGCATAAGAACACCATGAGAAGAAGAAGTATAAGTGGTTTCGTTCAAAGTTGAA\n+TTTATACCATCCGCCTTGTATCTTTGTTCTAAATAGTATGGATGACTTCCGTACATGTTT\n+TGGTCCACGGGGCTAGGTTCATCATTAGCCCAAAAGGTACGGGTTAAGTTATTTCCCAGA\n+CGTAAACCATGGATGGTTTCAGCGAGACCATAAAGATTATAATTTTCAACCATATTAGTA\n+GTTAACTCAATATACTGATCTTCGAAAACCAATTTCTGTCCGCGTGTATCAAATAAAACT\n+TCACCATCGCTCTTACGTGTAACCCAAAATTCGAAAGGATTGGCATTGTACGAAAAGTTG\n+TACAGAAGGTTTGTGTTATTGTAAGAAGGTGAATATAAGGGAGCATCCCAAAGATCTTTC\n+CTACTGGTAAATTGGAATTGAGTGTTATTAGCGTCTTTGATTGATATATGAACTCGGTCG\n+GCTTCCTCATATGTGACGTTGAGGAACAACAATGGGTAATCAGTACCATAGGCATAGCAA\n+GGCTCGCCGAGTAGTGCGAGATAGGCAGTAACGCCATTTTGTGACTCAGATATGTTAACA\n+GCTTGATATCCTTGACAATTTACACCGCGATATGGGTCATATACGGATAAGCGTTGAGGG\n+ATACCATTGGTAGGGATAGTGACATTGCGATCACCAATGACATTGAAAGTTTGGTAGACG\n+TTACCGACAGCAATCGAGATTGCTGAAAACAGAGCAGTTAAAAATAGAGATTGGTAGGCA\n+GTAGAAATCATCATCGTTAAAAAAAAACAAAAAAGAGATCAAAAAGTTTTAAGAAAAATC\n+AAAGTACCAACTAAAAAGAATCGTAGAGAAAAAGAATGGAAAAGATTAACCAAAAAGGCA\n+ATTTGGCAATAGAAGGGCGGTTTAAAGAGGCGAAATCGTAAAGAAAAGGAGGGTTTTAAG\n+AGACAGACAAAAAATTAAGCAAGAACTACAACAATAGAATTGTAGACTTTCTTGTCCAAG\n+TTTTTTTTTCAATATAAATAAAAAGTTATATATATATATGTGTGTGTGTATGTATATATA\n+TAGTAAGTTAGGAAAGAAAAGCTCTTTCACGAAAAGCTTGAAAGGGTTTGTTTAAACGCG\n+CGTTTTAAAAAGGAGCGAAACCCAAAAAAAGGTAAGAGGTAGGATTAACCAATCAAGTCC\n+AAAACGACGTAATTAAGAGCGGCTAAGCGAACCTTATAAAAGTGGGGGAGAAACTTTTGT\n+AGCTTGTGTTACTTAGCACTTTTTGCAAAACGAAGTGTATGTTCGCTTGAAGGTGCAAAG\n+AACGAGGAGGAAGCGAAAAGCCTTGATTAATTGATTTGATGGGTAAAGCCTTTGAAAGCC\n+AAGTCGAATCGAATCAATCTAAAAGCAAAAAAAAAGATAATCAAACCCAACGTTTAGTAA\n+CTTTTTTGTAAAAAAAGTAGGGCGATAGGTTGGAAAATGGATCGATTTTCTCGTGGGGAT\n+GGAATCAATCGACTCGTTTCTTTTGCAATGTGGGGAGACTTACTAAGGCGGATGTGGGGG\n+GAGGACAAAAAAACAAGTAGCAAAGAATCAAAACTTAACAAAATAAATTAAAGGTGTGGA\n+AGGTTTGAGAGCACTTCTGTTCTAGTGGAACAGATATTGCTTGGTTTTAATAAAGGGAGT\n+GGTGTAATCACAGGAGAAAACAGTAGGAAAACTATTGAGTTATACCCAACTGTGTTACCA\n+ATAGAGTACAGACACTGGAAGATTTCGGATCAAAAAAGTTGATGAAAACTTAGAACCAAA\n+AAGGCGCGAGGTATTCACTTGACTTATG\n+>TRINITY_DN217_c0_g1_i1 len=1840 path=[1:0-1839] [-1, 1, -2]\n+AAGAAATCTGCAGCTTAATTTGAAAACACTAAAAAAACCTGCATTCTTCTTTTTTCCACG\n+AAAGATCTGTTGCTGCTTACGCTATTATTTGTTATTATTATAAATAATAATAACATTTCT\n+ATCGATAACTTCGTTTCATATAGTTTTTAACATTTACTCCTTCCCACTTTTTTGTATAAT\n+ACTCTTCAAAAATGGCCCCTCAATTCAAACGCCCTGAGCTCTTTGGCTTTGATAAGTCTC\n+ATGCTCAATCTTTTGTTCAAGGAAAATGGATTTCTTCTCCTAACAACAAAACTTTTGAGG\n+TTGATAACCCAGCTACTGGTGAAATAATCGGTAAAGTGGCCGATGTCTCAGTAGAGGAAA\n+CAAAAAAAGCCATCAGTGCCGCTAACGAGGCCTTCAAAACTTATAAAAATTTTACTCATG\n+TCCAACGTAGTCAGTTATTGGAACGCTGGGCAGAGCTTATTATGGAGAACAAAGACGACT\n+TGGTCAAGATGCTTACCTTAGAAAACGGCAAGCCTTTGAGCCAAGCTGAGATGGAGGTCA\n+CCACATGTAGCGGATATCTTAAATGGTATGCTGCTGAAGCCGTTCGTACCTTTGGCGATG\n+TAGCTCCTTCCAGCTTACAAAGTCAAAACTTTCTCATCTCCATCAAACAGCCAGTTGGTG\n+TCAGTGCCTTGATTACTCCTTGGAACTTCCCCGCCGCCATGATTGCTCGTAAAGGTGGTG\n+CCGCTTTGGCTGCTGGTTGTACCGCTATTTTCTTGCCTGCTTTCCGCACTCCCTACGTTT\n+GCTTAGGTTTAGTCAGGTTGGCGCAAGAGGCCGGTTTCCCTGACGGTGTCTTAAATGTGA\n+TCACTTCTTCTGATGCATCTGCTCATGGTAAAGAACTGACTACCAACCCTATCGTTCGTA\n+AGGTTTCCTTCACTGGTAGTACTAATGTCGGTAAAATTCTTATGGGACAAAGTGCCAGCA\n+CAATCAAGAAGGTTTCAATGGAGTTAGGAGGTAATGCCCCTTTCATTGTATTCCCTGACT\n+TCCCCATTGATCAGGCTGTCGAATCTTTCTGCACTATCAAGTTTAACTCTTGTGGTCAAG\n+TTTGTGTCTGCCCTAACAGAGTTTACGTTCACAAGAATGTTTACGACGAATTCGTCAGCA\n+AGCTTACCGAAAAAGTCAAGACCATTAAAGTAGGAGATGGATTTGACTCTTCTTCTGCTG\n+TTGGCCCTTTGATTTCTCAAGATGGATGCAAAAAGGTCAGCAAGCACATTGAAGATGCTG\n+TTTCAAAGGGTGCCAAAATCACTGTTGGTGGAAAGGAGATTTCCTCAAGCAAAGGTTATT\n+TTTTTGAACCAACCGTGCTCTCCGGTGTAACTCAAGACATGTTGGTTGCTAGCGAGGAAA\n+CATTCGGCCCACTCGCCTCTGTCTTCAAGTTCGACGACACCGAAGAGGTGATCGAATGGG\n+CTAACGACAGTGATGTTGGCTTGGCCGGTTACGTCTTTACCAATAACTTGTCCACAATGA\n+TCCACGTTGCCAAAGAACTAGAGGTGGGTCTTGTAGGTGCCAATATCGAAATGGTTGACG\n+AACCATTTATTTCCTTTGGCGGCATCAAACAGAGCGGTTTTGGCAAGGAAGCCGGTCGTT\n+TGGGCGTTCAAGAATTTATGGTGGTTAAGGAAATCAATCTCAAGACTCTTTAAGGATTTT\n+CGCTTTAGAAAGCTGCATATTATTGAACAAGCAATGATGTCCTCTTTTGGTTAATGACTA\n+AAAAATCCTGATGTTATGACTGTTTTACATGTTTGCGATACAAATCGTATTTTAGTTTAA\n+TGATATCAAAAAAATTTAATACCTGAAAAAAAAAAAAAAA\n' |
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| diff -r 000000000000 -r 8605f8570c77 test-data/Sp_hs.left.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp_hs.left.fq Tue Jul 17 11:48:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,430704 @@\n+@61G9EAAXX100520:5:100:10004:15548/1\n+CGCCACGAGGTGCAGGGGGGATACCGGAAAGCTCAAACTTACCAAGCAAGTTACAGTCCTTGGTACGA\n++\n+GGFGGGFGGEEGGFEGGFBF?EGDFFE:GFF:G?EDEDEEECEE:EDE?E=EBBDEABCCACC=BECA\n+@61G9EAAXX100520:5:100:10005:5267/1\n+TCCCATGTTGAACAAAATCAATGGAATATCCATTGAATTCGTAATTCTGGTTCGAAATTCCTCCAATT\n++\n+GGGFGGGGGGFGGGGGFGGGGGGFFGGGGDFFFFFDEEEEFEFFDGGFEBDGBBFBDFEEABFDDA?E\n+@61G9EAAXX100520:5:100:10006:11985/1\n+TCCAGGGAGTTCTACATCAACGCTAACAGTGTCTTTACCCTCATGCACATCAATCGAAGGAGACAACT\n++\n+GGGGGGGGFGGGGGGGFGGGGEFGEFFFGFGGGGGGGGDGGGGGGFDFFGGEFGGE@EEDFDDBEDED\n+@61G9EAAXX100520:5:100:10015:8882/1\n+AAGAAGGGGTAGTGCGGTTACCTTGATCGTTGGCGATAATTTCGACACGGTTGTTGGAAAAGTGTCCA\n++\n+GFGGGGGGGFGGGGGGGGGDGGGGFGGFEDGEFEGEFEEGFEEEBDDDDDCDECEDDA=A=A7A<9@A\n+@61G9EAAXX100520:5:100:10018:4558/1\n+GTTGATAATACGGAGAACGTTCAAACCGGCAATAAGACCAGCATCCTTGGTGGCTTGACGTTGAGAGT\n++\n+FGGGGGGGGFGFGGGGGGGEGGFGGGF=GFGEGEGDFEEGEFBFEBEBDDADAD=CC:CC>CC4=5:2\n+@61G9EAAXX100520:5:100:10020:3719/1\n+TTGAGTCTTCTCAGAAGTGTCACCAGTCAAGACAGCAGCTTGGACGGCAGCACCATAGGCAACAGCTT\n++\n+GGGGGGGGGGGGFFGGGFGGGGGGGFGGGFGFGGGGGFFGGFAEGEEGFEBFBEEEEDEEC5DEB?CC\n+@61G9EAAXX100520:5:100:10036:2238/1\n+GGGGTAGCAAGGTTGTTCATGCGGATCATGTTGTTAACGTTAAAAGCACCAGAAACGTTTTTCAAAGA\n++\n+GGGEEGGGGEGGFGGGGGGGFGFFEGBFFEFFBEFFEDDEDEEBBDDCD?D?CCCB=AADDCCC:CCC\n+@61G9EAAXX100520:5:100:10036:9033/1\n+AGGGACTTCTCGACCTTGGGCAAGGTGACAGTCAATAGGCCATTACTGAAGTTGGCCTCAATGCGATC\n++\n+GGGGGGGGGGGGGGGGGGGFGGGGGDGGGGGEGGGFGEFGEEFFFEEFD@FCEDEEEEECDDEAE=DE\n+@61G9EAAXX100520:5:100:10038:14729/1\n+CAGGTCCATTGTCAGCACCGCCCGGAGCACCACCAGGGGCACCGCCAGGCATACCACCAGGTGCACCA\n++\n+GGGGGGGGGGGGGGGGFGGEGGGGFGEGGGFGGGGEDDDGFFFDFDEDCDADEDDDDEDCC;CADCCD\n+@61G9EAAXX100520:5:100:10042:17662/1\n+TCAGAATCAACAACACCCTTAATGAAACCCAACCATTCAGGAATCAACTCTTCACAGTCGTCGGTAAT\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEBGGGGEFBEFFFEEFEDEDDFBDCDCD\n+@61G9EAAXX100520:5:100:10045:11664/1\n+CTGTCATTGCCTCCTGTAGAGTACTTGTTAGGAGAGTAAGAAGAATCATCGTGTCTTCTCGAGTAAGA\n++\n+GGGGGGGGGGGGGGGGGGGGGFGGGGGGGGF5FEGGEEFFGDGEFFGGG??DGEDFFGEDBBDDD=EC\n+@61G9EAAXX100520:5:100:10046:4083/1\n+TTGGGGTTAATCTCAAAAGTCTTGCGGCTAGACATATAGGCACTCATAGAAGTATCACGAAGGGCTTG\n++\n+EGGGGGFGGGGGGGGGFGGGFGGFGGGGGGDEGGFFBD@EEFEEEBCECDDCAEDED:DCCC=?B>EC\n+@61G9EAAXX100520:5:100:10048:17127/1\n+TCAATGGCTTCCTTATCTGAAGCATCGACCTTATCCTTGAGATTAGGATCGTCCAAGGAATTACGAAG\n++\n+FFDFFFGGGGDGDGAEDEFFGG=GEGFFFGGGAGDGFEEAED?EEBEDEFGDFGDBEAD?EEB?E@A?\n+@61G9EAAXX100520:5:100:10049:14013/1\n+CTTGAACGTCCTCTTTCTTAACACCAAGGAGTTCTACATCAACGCTAACAGTGTCTTTACCCTCATGC\n++\n+GEGGBGGGGGGGGGFGGGEG?FFFFDEBDEFFGFGGCEGFADEBFFEEEGE@FDBFCEDBDEBFDEE:\n+@61G9EAAXX100520:5:100:10055:6276/1\n+TCCTGGGAGTAGAACTCTTGGGAAGTACAATGAATCCACGCTGTAGACAGTATCTAATCATGATTTGA\n++\n+GGGGGG?GGGGGGGGGGGGEGGFFGGGGGGGGGGGEFGGFGFCDFBEDEFCEFBG=CECECEDA@CDC\n+@61G9EAAXX100520:5:100:10064:17140/1\n+TCAATGGCTTCCTTATCTGAAGCATCGACCTTATCCTTGAGATTAGGATCGTCCAAGGAATTACGAAG\n++\n+>C5>AAA:A>=:DDAAC=-5CCCCCA5AACCC-?,A:BA-D=5BDC-DDD>:B:ACC:-@:CA5A?B?\n+@61G9EAAXX100520:5:100:10072:2848/1\n+TGAGAGATGAACTCACTGTGTTTCTTGACGGTATCTTTGATAGTCTTTTCCTCGAGGTATTGAAGTTG\n++\n+GGFGGGGGGGGGGGGGGFGGGGGFGGGGGGGDFGGGGGGEGGDDGGGGGGGFFGBDFCFEFF:DEAEE\n+@61G9EAAXX100520:5:100:10075:9308/1\n+GGGAATACGGGTGGAACCACCGACTAAAACAATCTCGTTGACGGAGGCCTTGTCGACCTTGGAGTCAC\n++\n+GGGGGGGGGGGFGGFDGGGGGEGGGGFEFFGCGDFFGCEEDDEDCDDDCCDBCD?BCDDCDA@EADC@\n+@61G9EAAXX100520:5:100:10090:12439/1\n+AGAGCGGGCTGCTTTGCTTGAAACAGTCTCAGTGGTGGCAGGATAGTGATAGGCGGCGGACTTGCTCT\n++\n+EGGGGGGGGGGFGGFGGGGGFGFGDDFGGGBGDFGCGEEEGE:DDEBECACCEA##############\n+@61G9EAAXX100520:5:100:10115:15451/1\n+GCGGTCTTCGGCACCATTCTCCTCAACCTTCTTCTTGAGCTCAGCAATGATGGGAGACTTGGGGTTAA\n++\n+GGEDGGGGGGFFDGGFGFGGGGGGGFGGGGGGGGEGAFDEFDAAFDFDEDEDDACEC?CEECEEAECC\n+@61G9EAAXX100520:5:100:10117:17047/1\n+GCCGGAAACTTGAGGAACATCAAATGTGAAAATCGTGTTGGTATGATTGTTTTGCTTCTGAAAGACGA\n++\n+EGGDGEGGGEGGGGGGGGGGGGGGDGFFGGGGGFGEGFGGGCGFGDGGFEFGGEFEEGGGB:AFDEB:\n+@61G9EAAXX100520:5:100:10124:13659/1\n+TTTCCGCTATCATAATGGACTTGAACGTCCTCTTTCTTAACACCAGGGAGTTCTACATCAACGCTAAC\n++\n+GGGGGGGGGGGGGGGGBGGFGGGDGGGFFFGGGGGFGGEFFEEEDEEDCEDDDD?BDEDDBBEEECCD\n+@61G9'..b'+GGGGGGGFEGGGGGGGGGGGGGFGGGGGGDEEDCFGFEFEBEEE=DEEEDBBF:DEEBBC@A?5B&9A\n+@61G9EAAXX100520:5:1:11086:4349/1\n+CTGGAATAGTAATGGTACGAGAGAATGAGCCAAAGCGACGCTCTGACCAGCGTTGGGTACCCTCGGAG\n++\n+GGGGGGGGGGGGGGFEFFGGGGGDGGDDE?FFGB?GEFFE=F=G:BE:B=?C7:@#############\n+@61G9EAAXX100520:5:1:11101:19670/1\n+CTTAATTACTCGATGGAACCTTGAACCTTTGTAGGTTAAACAACGGCCATCCTTCTCACACCCATTAC\n++\n+GGGFGEGGGGEGGFFFDGEEFGD=G?B=GFF?BEEBEEBBB;<BB=BBBAA@=B=BAA5B?=??,:??\n+@61G9EAAXX100520:5:1:11102:11642/1\n+CTCGTTGACGGAGGCCTTGTCGACCTTGGAGTCACGGAGAACACGCTCGACGGGCTCCATGGTTTTAC\n++\n+GGFGGGGGGGGFFFCGEFCBFGDEGGEEGEGDEDEFBBDBFCEE?EEEEDCC?CBDDEBCAA<:5<:>\n+@61G9EAAXX100520:5:1:11104:15532/1\n+CATGAGCTCAGCAATGATGGGAGACTTGGGGTTAATCTCAAAAGTCTTGCGGCTAGACATATAGGCAC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGFGGGFFGGEFFEFBGEEEEDFDBEDD@DCD:5?58AA?A5?9C?1\n+@61G9EAAXX100520:5:1:11108:14219/1\n+GTGTAGAAGTCAATACCCTCGAACAAAGAGTCAATCTCAATGCTAGCTTGAGCAGAAGAAGAAAGAGT\n++\n+GGGGGGGEGFGGGGGFGGGGGGGFGDGDEGDGFCFFBEFEGBEFDGFGEDDDEDDCDECDCDD?DD@:\n+@61G9EAAXX100520:5:1:11110:2201/1\n+CTAGAGATCACTTGCTCATCATTGGAGAATCGTAACAAGTGGTAGTCAAGATCATTAAAACACTGTCT\n++\n+FGGGGGGGGGGGGGGGGGGGFGFFGBG:DFGFDFEFFCEBEECDECBCDD?,@@ACC?5:5??A7:?#\n+@61G9EAAXX100520:5:1:11119:3103/1\n+GGCAGCAGTAACCAAGGCACGGTCAGAGATAGTAACACCATGATGAACCTCACACTTTTCTTTACGAC\n++\n+B?55DBD:D?DDD-=C5?==DADA5=5DAB?C>ACCDCBDBCBCB5BBB:C5-@?5?5B@@821524@\n+@61G9EAAXX100520:5:1:11161:10524/1\n+CCCCTCTCCACTTCACCCAAGGCAGATTTTTTGATTGAATGGTCGTCGAATTTACATTTTCCTGTTTC\n++\n+FGGGGGGFFGGGGGGGGGGFDEGEGDAGGGGGEDGGEFBEDDC5ECAA=5CCCCC:@=AA<CC5A?##\n+@61G9EAAXX100520:5:1:11169:2823/1\n+CAAGAGTGAAACCAGAGGACAACAAGGCGGTCTCATACAAAATAGTAGCAAGATCCTTCACAGAGCGG\n++\n+FEFFFFFAADFFDBFFFB:AEEEEBE=?E?EFFFE?:BA?B<C?36>=>>DDEDBD@?FA:?5????#\n+@61G9EAAXX100520:5:1:11178:16777/1\n+CTTGAACGTCCTCTTTCTTAACACCAGGGAGTTCTACATCAACGCTAACAGTGTCTTTACCCTCATGC\n++\n+GGGGGGGFGGGGGGGEGGGGGFGGFGGEGFGDDGGGFE?GEDEFEF=?DGEBCEEEDEECDEAGDEEB\n+@61G9EAAXX100520:5:1:11179:14447/1\n+GGTTGATGGACTTGCAAGGCTCCTTACCGTTGAAGAAGTCAGAGACAAGCTTTTGAACACGGGGAATA\n++\n+FFFFF?FFEFEFF=BEBEEE?DDFA=ECBADEBDDCB:BBDAEA:CCCCCA?@AD-==5@A=<C####\n+@61G9EAAXX100520:5:1:11182:5055/1\n+TTAACAAGCAAGGAGAACCAACAATCTTGTTAGAAACAACAACCTTTTCAACCTTGTCACCCAAAATG\n++\n+FFGDGGEGGGGFFFGCFGGDGGGGGDGGBFGFCDEBDFFEGEDFEDDFEEECDADDCDDCBDCC??C?\n+@61G9EAAXX100520:5:1:11183:5436/1\n+ATTCAATTGTAGTCCAGACACCGATATGTGAAAGAAATTGGTAAGAAAAAGGAAAATGTTTGCTTTGT\n++\n+GGGGGGGGGGGGGGGFGFGGGGGEGFGEEFFEGGFECGGEECEBFEDD=C@BDDEDDDCDEDBFCBB2\n+@61G9EAAXX100520:5:1:11185:15634/1\n+CTCGAGGTATTGAAGTTGGTCTTCTTTCATGAAGAGACGAATCTCGGTACCACGTAACAAGCGAGGTC\n++\n+GGGFGGGFGGGGGGGGGGGEGGGGGGFGFGG=EGEADCFE?BAEEEDCDDB@CD@==AA?AA5>:?:A\n+@61G9EAAXX100520:5:1:11190:8705/1\n+GGTTGATGGACTTGCAAGGCTCCTTACCGTTGAAGAAGTCAGAGACAAGCTTTTGAACACGGGGAATA\n++\n+EEBEEEEEEBEEEEC?EEDEBEEEEBEEDEEAE?D=B?@=@=?A@@?@:BBEBBB:@?BB???B1=22\n+@61G9EAAXX100520:5:1:11201:16392/1\n+GGAAAGAGAGGTCAAATATTGACCATCAGAAACCACAACATCACCTTGAACGGACTCAATTCCATTAA\n++\n+GGEGFGGG=GEDGGFFGEBF=BFEDADEFEBDAEEFDAED@DD?@=B=@ABB@BB@B5B:3?######\n+@61G9EAAXX100520:5:1:11207:13415/1\n+GTTGTAACGCAAAAGCTTGGCTAAAGCAGGGCGGTTAGCAGCATCCTCATGGATACCAAGCTTCAAAT\n++\n+GGGGFGGGGGGGGGGFGFGGGGGFFEGFFDEEGB:E:CEEEDDEDDEB?FDD=CCA>,?<A??<:4AC\n+@61G9EAAXX100520:5:1:11230:2458/1\n+GTTTTGGTAAGATGGGTTGGATCACCTGGGCCGTTAGTCAAAAATATGCCATCGTAATTGCTAGCAAC\n++\n+GGGGGGGEFGGGGGCFDFGEFEFGGDDDDEGEDDDCECEDCDDCD@@CCCB=C=B:<A??>A<C?C?C\n+@61G9EAAXX100520:5:1:11234:3959/1\n+TTCGGCATCCTCAGCGTCACGGACCTTCTTGGTGAGCATGGCGAGCTGTTGACGAGAATCAACGTCAA\n++\n+GGGFCGGGGGFGFE?GGGGGGGEGGGGGGGEFEFEGGFDFDGDDFGDGDD=DBE:E:AABDBGEBA@:\n+@61G9EAAXX100520:5:1:11240:13099/1\n+TGACGGAGGCCTTGTCGACCTTGGAGTCACGGAGAACACGCTCGACGGGCTCCATGGCTTTACGGAAG\n++\n+EEEEE?5EDDE=EEEEE:BE:-A?>C9C?:C->=@CBCE?BB=E5@?-:?@?EBA:5-=5?:?#####\n+@61G9EAAXX100520:5:1:11244:13063/1\n+GCAATGGGAATCGAAGAAAACTTCATGGTGCGTGTAATAAAAATCCAAGATTTTCAATGAATAGATGC\n++\n+GGGGGGGGDGGFGGGGGDFGGGGGDGGFCDGEFGDFDGD?ECCGFGGEEFGEEEGGDGEDABEEDABB\n+@61G9EAAXX100520:5:1:11248:13248/1\n+CCCAGATATTCTCAGATGCCAAGAATTAAGTGCTCATTTGTATAGGGTAATTAGATGTATTTTGATCG\n++\n+DDDFGGGGEFGGEG:GDDDGGAFB?DEEBEB:EF?FDEGEE=A=BA??5=C5?@BDBBEEE?B3B@?#\n' |
| b |
| diff -r 000000000000 -r 8605f8570c77 test-data/Sp_hs.right.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp_hs.right.fq Tue Jul 17 11:48:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,430704 @@\n+@61G9EAAXX100520:5:100:10004:15548/2\n+GACTGGTGACACTTCTGAGAAGACTCAAGATCTTTTGTTGCTTGATGTTGCTCCCCTTTCCATGGGTA\n++\n+EGGGGGDGGGGGGGGGEFGFGGFGGFDGGGGDGGGGGFGGGGFFGFGDFFGGFFFFEEEAFEFEEEAA\n+@61G9EAAXX100520:5:100:10005:5267/2\n+GTTGTGACTTTGTAGACGTTGAGCTTGGTTGGAGTTCTGAAACCATCAATATTCTTTATCAACACAAG\n++\n+GGGGGEGGGGGGGGEGGGGEGFGGFGGGDGBDFFEFGGGDFGFGGGEEGEFEEEGFGGEFEFF=EDDF\n+@61G9EAAXX100520:5:100:10006:11985/2\n+TTTGAATTGAATTCATATAATTTCAAGTTACTCGCAATTGTTTAAATTTTAAAAAATGTCTTTGCAAC\n++\n+GGGGEGGGGGGFGGGGGGGGGGGGGGGFGGGGGFGGGGGGEGDGFFGGGGGGGGEEGGEFGFGFGFFG\n+@61G9EAAXX100520:5:100:10015:8882/2\n+TTAAGGAGTAATAAATCATTTTCCTTATAGGAAGTTAACGAAGAAAGTTATCTATTGCATCTTAAATA\n++\n+GGGGEGFGEFGGGGGGGGGGGGFGGGEGGFFEEGEGGEGGFFGDEEFCF?GFFFFFEFFFEGF:EDFF\n+@61G9EAAXX100520:5:100:10018:4558/2\n+CGGCCGTAAATTTGATGATCCTGAGGTTCAGTCTGACATGAAGCACTGGCCCTTCAAGGTCATCTCCA\n++\n+FGGGGGFEGFGGGGGGFGGGGGGFGDCFGGGGGGGFGGGGGGDGGEEEFGGGFBFDFEDCEDFEFGE=\n+@61G9EAAXX100520:5:100:10020:3719/2\n+CTCCATTACTCGTGCCCGTTTTGAGGAGCTTTGCGCCGATCTCTTCCGTAAAACCATGGAGCCCGTCG\n++\n+GGGGGGGGGGGGGGGGFGGGGGGGG?GGGGGGGFGGGGGGGGGGGFGFFGFFFGEGEFBEFGEBECGF\n+@61G9EAAXX100520:5:100:10036:2238/2\n+CGCGTACAAGCTGCTTCCAACTGCTCCAGCGGCCCTTACAATATCTCCGCCCAAGGTACTCTTGACGA\n++\n+GGGGGGGGFGEGGFGFGGGGGGGGDGGGGGGGGGGGFFGGGGEGGGGGGGFGBBED?FFFDGD??B?E\n+@61G9EAAXX100520:5:100:10036:9033/2\n+CGGAAAACTTACTATTTCTGGCGAAGTCGTCAATGAGAGAAAGAATGAAAGCACCGAGGGTAACCAAC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGFGFGFGGGGGGGFBGGGGEGGGGGGFGFCDDDFCBAD\n+@61G9EAAXX100520:5:100:10038:14729/2\n+TGATCGTATGGTATCTGAAGCCGAGAAGTACAAGGCTGAAGATGAAGCAGAAACTTCTCGTATTCAAG\n++\n+GFGGGGEGGDDEGGGGEGGGGGGFGGFEBFFFEEEGBGFFEEDEEDDGGDFDFBDBEFEECEDDCED?\n+@61G9EAAXX100520:5:100:10042:17662/2\n+GAAGAGTATGCCTCTTTCTACAAGTCTTTGACTAACGACTGGGAAGACCATTTGGCCGTCAAGCACTT\n++\n+GGFGGGGGGGGGGGGGEGGGGGDGFGEGGGDGGGGGFEGFEECFGFGEGGGGFDBEGGDEGGEDEG?B\n+@61G9EAAXX100520:5:100:10045:11664/2\n+CAGCTCAAGCGCTGGTGCTGTCCACAACAGTGATGAGCCCTTCTCTTCTAGTGGTGCCCCTCAAAATC\n++\n+GGGGFGGFGGGGFGGDGGGGGGGGGGGGFGFGGGGGGGGGGFGGFGFGGGBDFFDGGFEGEGGDGFBF\n+@61G9EAAXX100520:5:100:10046:4083/2\n+TCAAGGAATTCGAGGGCAAGAAATTGGTTAACATTACTAAGGATGGTCTTGAGTTGGAAGAGACTGAC\n++\n+GDFGGEGGGGGGGGGGFFFGGGGGGFDDFGGDGGGFGGGGGGFGGGEGFGFEGDGFEFGDEA:FFFF=\n+@61G9EAAXX100520:5:100:10048:17127/2\n+TTGAGCTTTCTGGTATCCCCCCTGCTCCTCGTGGTGTTCCACAAATCGAGGTCACCTTCGATGTTGAC\n++\n+GGGFGGFGGFGG??GFGGGGGG?FGGEGGFFEGGFGFDGGDDDFGAGFDAFBF=FFGGFEDDFD?=A5\n+@61G9EAAXX100520:5:100:10049:14013/2\n+TTTGAATTGAATTCATATAATTTCAAGTTACTCGCAATTGTTTAAATTTTAAAAAATGTCTTTGCAAC\n++\n+GGGGGGGFFDGGGGGGGGGAFGGGGGGFGFEGGDGGGGGGEGGGFBGGGGGGGGEGFFFGEGEEFGEG\n+@61G9EAAXX100520:5:100:10055:6276/2\n+GCGTTTCCAACTTTGGTCCTCATCACATCCAGGAATTGTTGGACAGCCATCCAAAGATTATACCATGT\n++\n+GGGGGGGFGGGGGGGGEGFGGGGGGGGGFGFGGEGFGGDEFEEEFGGGGEGBEEEGDEEFEEEDDCA5\n+@61G9EAAXX100520:5:100:10064:17140/2\n+TTGAGCTTTCTGGTATCCCCCCTGCTCCTCGTGGTGTTCCACAAATCGAGGTCACCTTCGATGTCGAC\n++\n+EEDE=?DAED?E?AEEDEDEEEDADEEEEDA:AC=DDDCD?DA-E?B:=C,5C:?C5@:A########\n+@61G9EAAXX100520:5:100:10072:2848/2\n+GCATACTTGGTTGCCGACAAGGTCCAAGTCGTAAGTAAGCATAATGACGATGAGCAATACATCTGGGA\n++\n+GGGGFGGGGGGGGGGGGGGGGGDGGEFGGGGEGGGDGGGGGGGGGGGGDGGGGGGGGGGFGGEGFFFD\n+@61G9EAAXX100520:5:100:10075:9308/2\n+CAAGAACAAGAAGGATATCACCGGTAACGCTCGTGCTGTCCGTCGTCTTCGTACCGCTTGTGAGCGTG\n++\n+GGGFGGGGGGGGGGFFGGGFFGGGDGGFGFDFGDGEEEDEFFDFDDEFEEEDEEDDCDDDDBADCCBC\n+@61G9EAAXX100520:5:100:10090:12439/2\n+TCGAGGAAAGCAAATTGACTGACTTGCGCACTGCCGAGCCATCCCAGTATGTCAACGACGTAGAGGTT\n++\n+GEGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGFGDDFFEAF=GFDECDGEBDBA?\n+@61G9EAAXX100520:5:100:10115:15451/2\n+GGAGTTTGCTAAGCAACTTAAGACCATTTTGGGTGACAAGGTTGAAAAGGTTGTTGTTTCTAACAAGA\n++\n+GGGGGGGGGGFGGGGGGGGGFFGGFGGGGFGGFDGGFGEGGDGGEEEFFECGFCGGDGFGGFEBBEDE\n+@61G9EAAXX100520:5:100:10117:17047/2\n+TTCTAGTTCAGCTGCTACTTCAACTTCAACTCGCGTTTCATCGTCTGCTAAAGCAAGCACTTCTAGTG\n++\n+GFGGGGFGGGDGGFGEFGGGGGGFGGFFBGGCGGGEGDFGGDEFGGGGEF?FEEE:EEEE@DDDDB:B\n+@61G9EAAXX100520:5:100:10124:13659/2\n+TTTGAATTGAATTCATATAATTTCAAGTTACTCGCAATTGTTTAAATTTTAAAAAATGTCTTTGCAAC\n++\n+GFGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGD=GGGGGGGGGFEGFGGFFGEGGDGFGGGBBEF\n+@61G9'..b'+GGFGGGGGGGFGGGGBGFBGGGG=GGGDGDGDGGGFGGGF:BEDEFEEFBGGFEGGFGFBEADD-@4C\n+@61G9EAAXX100520:5:1:11086:4349/2\n+TTTGAATTGAATTCATATAATTTCAAGTTACTCGCAATTGTTTAAATTTTAAAAAATGTCTTTGCAAC\n++\n+GGGFGGGGGFGGGDGGGGGDGGEGDGEDGGEGGFD:EFFDGGG>GFEFEGEFE:EFF?DECB:+EFDF\n+@61G9EAAXX100520:5:1:11101:19670/2\n+GTAAAATCGCTCTTCATTCTTCTTCTTAAAGCAACTTTGTGGTGTGAATACACTGAGGAGACTGGCAG\n++\n+FDAFBEDDFEE-ECEEFD5DFFBFFEDFFFDFF5EE=EE:DEBE,B@?@CFCF:A?CA?E5??B?ECE\n+@61G9EAAXX100520:5:1:11102:11642/2\n+CGTGCTGTCCGTCGTCTTCGTACCGCTTGTGAGCGTGCTAAGCGTACTCTTTCTTCTTCTGCTCAAGC\n++\n+GGFFGGFGFGFEGGDF?FFFFBGGEGF?CCEBEEGCA-DF=AA?@D?D?EFDBEDDBEB?5BBBB?A#\n+@61G9EAAXX100520:5:1:11104:15532/2\n+TTTTGGGTGACAAGGTTGAAAAGGTTGTTGTTTCTAACAAGATTGTTGGTTCTCCTTGCTTGTTAACT\n++\n+GGGGGGFFGGGDFGGFGFGGFGGDEBGGGGGGGFFGFGAGG=GEAGGG?FGEFBFGFG=GEAEG:?A=\n+@61G9EAAXX100520:5:1:11108:14219/2\n+TGAAGTTAAGGCCACTGCTGGTGACACTCACTTGGGTGGTGAGGACTTTGACTCCCGTCTTGTAAACC\n++\n+GGGGGGFGGFGGGGGGGFGGGCFGGGGGGGFGGGFGCGGCECEE=DEEFEBDEGEEFCFFE=BA=CA5\n+@61G9EAAXX100520:5:1:11110:2201/2\n+GATTTTAATATGATAGTTTCGAAATGGTTATGAGACCAATCTTGTTGGATTGTGAGCATATATTATTG\n++\n+GEGGGGFGGGGGGGGGEGGGGGGAGGGEGGFGFFGGGGFGGGGGFGGBDGEFABEBB?55A@B?@FE4\n+@61G9EAAXX100520:5:1:11119:3103/2\n+GGACGCTGCCAATTTGCTGAAGCCAATGCTTGCACGTGGTAAGTTTCACTGTATTGGTGCTATTACTT\n++\n+55:BBAAB:ABB@@?D?=C:=CC5C:D:ABB5C-A55>=+>>;;;55>=>????C-..;;@@=@-?:C\n+@61G9EAAXX100520:5:1:11161:10524/2\n+GGAAAAGTACTTCTCGTGGCAAGCAGTTACTATGGACCATTTTATCCAGATGGAATGAATACTGGAGT\n++\n+EEEEEEEEDDEEEEEEEEB=D=??ECE=BEC:ED?DEB?DEBEE>EEBBB5BAB?5C:???55C===A\n+@61G9EAAXX100520:5:1:11169:2823/2\n+CTTAAGACCATTTTGGGTGACAAGGTTGAAAAGGTTGTTGTTTCTAACAAGATTGTTGGTTCTCCTTG\n++\n+FEBBBB?F@EEBFEFDFE?FDED=EBEBE?EDED5EEBEDEEEB?EAAE;BEEE=?ADD:?DEEE?EE\n+@61G9EAAXX100520:5:1:11178:16777/2\n+CAGATTTGAATTGAATTCATATAATTTCAAGTTACTCGCAATTGTTTAAATTTTAAAAAATGTCTTTG\n++\n+GFGGGGGGGGGGGGGGGGGGFGGGGGGGGFGGGGEEGGGGGGGGEGGEE?GDGGGGGGFDDGEGGGD?\n+@61G9EAAXX100520:5:1:11179:14447/2\n+ATTCAAGCGCAAGAACAAGAAGGATATCACCGGTAACGCTCGTGCTGTCCGTCGCCTTCGTACCGCTT\n++\n+FGGGGGDGGGDFFFFGGGGEGFDADFFGAEGGBDBFGBFBGGDFGDFBDFAAA@)?A<>:8@?#####\n+@61G9EAAXX100520:5:1:11182:5055/2\n+GCAAGCCGTTGAGAACTCTCCCTTCTTGGAAATCTTCCGTGCCAAGAAGTTTGATGTTCTCTTCATGG\n++\n+GGGGGGGGGGGGGGGFGGGGGFGFGFGGGAGGFGEFGGGGCDEGAFDBGEFEFDEDA=EFEEB5@?A5\n+@61G9EAAXX100520:5:1:11183:5436/2\n+GAAAGTTTGTTGATGATGATAAAGTGGTCCATCATGAATTTGTTTGGGCTTTTGACGTTGCAAAAAGC\n++\n+GGGFGGGGGGGGGGGGGGGGGGGGEGGEFDGGFGGDBEGGFGGGGGDDGGGF=DEBAFEGFDGGF?DE\n+@61G9EAAXX100520:5:1:11185:15634/2\n+GGAAGCTGCTGCTTCTGGTGCTGATATCTCCATGATTGGTCAATTCGGTGTTGGTTTCTACTCTGCAT\n++\n+GGDGGGGGGGFFGFFGGGEGGGGGFFGGGGGGGFDGFFGCGEGGEGGDEGEGGGEFGFFGFGGEGGDE\n+@61G9EAAXX100520:5:1:11190:8705/2\n+GTTCTCCGTGACTCCAAGGTCGACAAGGCCTCCGTCAACGAGATTGTTTTAGTCGGTGGTTCCACCCG\n++\n+EEEEDE?EBDDEEEE:D?B?EECCDBEBEEEEED?EDEDEDDEEEEEEE;A=@EEE?EEEB=EEE9ED\n+@61G9EAAXX100520:5:1:11201:16392/2\n+CCTTTTTGCATCCTAAAAACTATCTTTCGTTATATTTTTCCAATCATATTTCTACATAATATAGTCTA\n++\n+GGGGGGGGGGGFGGGGGF?GFEGEGGGGGGGBDEEGGGEGFGFGGFAB=GGGAGG:EEEEFFF:EEA?\n+@61G9EAAXX100520:5:1:11207:13415/2\n+CGACGACTGTGAAGAGTTGATTCCTGAATGGTTGGGTTTCATTAAGGGTGTTGTTGATTCTGAGGACT\n++\n+GGGGGGDGGFGFFDFGGFFFGGGGGGDFGGFGGGGGGFEGGGDDAEEECDEAEEEEEDC5==BEEDEF\n+@61G9EAAXX100520:5:1:11230:2458/2\n+GAAGAAGTGAATTTAGTTAGCCAGGTTTCCACCCGTGAGCCTTTCTTCGTCAGTGGCGGAGATGGCAT\n++\n+GGFGFGGEGG?FFFFGGGGFGGGFGEGGGGGGGGGEFGGGGFGGGGGGGDGFABGEDFDA########\n+@61G9EAAXX100520:5:1:11234:3959/2\n+CGGAAATCGACGTTTACAGAAGCAGCGTCGAAAAGACCAAGGCCGAGCTTGCTAGCTATCAAAAGGGT\n++\n+GGGDFGGGGFGGFGGEGGFGGGGGGGGDFGGADGFFGFGFEDB?FEE?ABFEEF?CBAFGFD5FB:A0\n+@61G9EAAXX100520:5:1:11240:13099/2\n+TTTGATGTTTCTCTTCTTACCATCGAAGAGGGTATCTTTGAAGTTAAGGCCACTGCTGGTGACACTCA\n++\n+5?FBEBE:=B5@ADB5:CD:=BEEE--DD-:C?ADDECCEA-D5AB?@?:?:A:A5:-><+==3B>(A\n+@61G9EAAXX100520:5:1:11244:13063/2\n+CGAAGCCTTACTAAACAAAGTAAATAAGTCTTCATCAATTCCCTTTAATCTCTCATTATAATTATTAT\n++\n+GGGGGGGGGGGGGF=GFGGGEGGGGFDBBFGGGGGGGFGGGGGGGFGDFGBGGEGGFFGEBGGGGGGG\n+@61G9EAAXX100520:5:1:11248:13248/2\n+ATAAAAATGGAGGCTAGACAGTCAATTGCTGACTTGTCTTACAAAATCACCAATCTTCTTCCTATCTC\n++\n+GGEDGD>C?CFDBBBABDEAF?EF?ED5EBADDDGGBEA=EBGD?FFEABE:EBEBDD5=?E:ABBA5\n' |
| b |
| diff -r 000000000000 -r 8605f8570c77 test-data/reads.left.simPE.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.left.simPE.fq Tue Jul 17 11:48:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,226068 @@\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap226-1/1\n+GGGCGGCGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap227-1/1\n+GGCGGCGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAAT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap228-1/1\n+GCGGCGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap229-1/1\n+CGGCGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap230-1/1\n+GGCGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap231-1/1\n+GCGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap232-1/1\n+CGGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap233-1/1\n+GGGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap234-1/1\n+GGCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap235-1/1\n+GCGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap236-1/1\n+CGGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap237-1/1\n+GGGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap238-1/1\n+GGGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGCG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap239-1/1\n+GGCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGCGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap240-1/1\n+GCGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGCGGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap241-1/1\n+CGGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGCGGCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap242-1/1\n+GGCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGCGGCCG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap243-1/1\n+GCGCTCGGGGCTCGGCTGGCCTCGGCTCGCCTCGGCTGCGCTCGGCAGGCTGCGGTAAATCCGGGCTTGCGGCCGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n'..b'198B|ENSG00000182796.8_Bp1831/1\n+CAGGGAGTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1832/1\n+AGGGAGTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1833/1\n+GGGAGTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1834/1\n+GGAGTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1835/1\n+GAGTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1836/1\n+AGTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1837/1\n+GTGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1838/1\n+TGACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1839/1\n+GACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1840/1\n+ACCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1841/1\n+CCCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1842/1\n+CCACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1843/1\n+CACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1844/1\n+ACTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCAGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1845/1\n+CTGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCAGCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1846/1\n+TGGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCAGCCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1847/1\n+GGGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCAGCCAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1848/1\n+GGCCTCATTGCCTACCTCAGCCACTTCCACAGTGCCTTCAAGAGCATGGCCCACAGCCCAGGCCCTGTCAGCCAGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n' |
| b |
| diff -r 000000000000 -r 8605f8570c77 test-data/reads.right.simPE.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.right.simPE.fq Tue Jul 17 11:48:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,226068 @@\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap226-1/2\n+GACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGTAGAGCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap227-1/2\n+GGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGTAGAGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap228-1/2\n+GGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGTAGAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap229-1/2\n+GGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGTAGA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap230-1/2\n+TGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGTAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap231-1/2\n+GTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGTA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap232-1/2\n+CGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGGT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap233-1/2\n+CCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap234-1/2\n+ACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap235-1/2\n+GACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGACA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap236-1/2\n+GGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGAC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap237-1/2\n+CGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCGA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap238-1/2\n+ACGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGCG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap239-1/2\n+CACGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap240-1/2\n+CCACGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap241-1/2\n+TCCACGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap242-1/2\n+GTCCACGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@B3GNT1|ENSG00000174684.6--NPSR1|ENSG00000187258.9_Ap243-1/2\n+GGTCCACGGACCGTGGGGACGGGGGAAAGAACTCAAAATATTGGTCTTGCTCCTCCTGCCCGTGCAGTCCGGACAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n'..b'198B|ENSG00000182796.8_Bp1831/2\n+ACCAGCATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1832/2\n+CCAGCATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCAC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1833/2\n+CAGCATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1834/2\n+AGCATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1835/2\n+GCATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1836/2\n+CATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1837/2\n+ATCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1838/2\n+TCCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1839/2\n+CCTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1840/2\n+CTCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1841/2\n+TCTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1842/2\n+CTGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1843/2\n+TGCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCCT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1844/2\n+GCATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCCTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1845/2\n+CATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCCTGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1846/2\n+ATTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCCTGGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1847/2\n+TTTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCCTGGGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@MICAL1|ENSG00000135596.13--TMEM198B|ENSG00000182796.8_Bp1848/2\n+TTTCCTTGGCCCGGGATCGCTGCAGGGTCCTCTGAAGTTTACTAAGGAATAATACAGCACTGGAGGTCCCTGGGGA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n' |
| b |
| diff -r 000000000000 -r 8605f8570c77 test-data/reads.simPE.Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.simPE.Trinity.fasta Tue Jul 17 11:48:59 2018 -0400 |
| [ |
| b'@@ -0,0 +1,770 @@\n+>TRINITY_DN2_c0_g1_i1 len=203 path=[361:0-202] [-1, 361, -2]\n+GTCCCCCTACCTCAAGAGCCTGTCCATGGTGACTGCCAACAAGTTGCTGCACCTGCTGGA\n+GGCCTTCTCCACCACCTGGTTCCTCTTCTCTGCCGCCCAGAACCACCACCTGGTCTTCTT\n+CCTCCTGGAGGTCTTCAACAACATCATCCAGTACCAGTTTGATGGTCCAAGTCCGAGGGC\n+AGCACGCGGCCCGGGAAGCGCTG\n+>TRINITY_DN2_c0_g2_i1 len=203 path=[181:0-202] [-1, 181, -2]\n+AGCGCCGCGGACACCGGCACCGGCGCCACGGACTCCGCAGGACCCCGCGCCCGCCGCCGC\n+CGCTATGCTGGGGCTGCTGGTGGCGTTGCTGGCCCTGGGGCTCGCTGTCTTTGCGCTGCT\n+GGACGTCTGGTACCTGGTGCGCCTTCCGTGCGCCGTGCTGCGCGCGCGCCTGCTGCAGCC\n+GCGCGTCCGTGACCTGCTAGCTG\n+>TRINITY_DN14_c0_g1_i1 len=881 path=[859:0-880] [-1, 859, -2]\n+GGCCCGTCTCTTTGTAAGTAACTTTATTTTTATTTACAACAGAATTGGTGGCTTTATTCC\n+TCCATCTTTAGGGACACTTGGCATTAGCAGCTAGATGGAAAGTCCGCAGTGAAGTCAAAC\n+TCATTCTGCCCCAGCCACAGCTCCGGAAGCTCATTGGCTCGGTCCAACCCCAGTTCCACC\n+ACCAGCGACATCAGCACTTCCTCATCCACTGGGTCCGAATCGATGATAGCAGGGCTCTGG\n+GCACCAGCAGAAGGAGAGAGTGATTCTGCCCCTCCCGCCTGGGCCCCAAAGTCCCAGTTT\n+TGCAGGGGTCCTGCCTCCCCGGGTTGGCCTGGAGTGGCAGCAGCCATCCCCTGATACTGG\n+CTATTAAGTTTCTGCAGGTGCATACTAGCCAGCAAGTGAGGGGCGGGGTGCAGGTTGAAG\n+GATGGGGGTTTAGTGGGAGGGGTGGTTGTAGGAGAGCCTATTGGAGATCCCGAGGAACTA\n+GTGGGAGCCCCACTGGCCTTGGTTCCATTTGAGGCTACCCCAGGGTAGTGCAGAATGGCC\n+ACTGCTTTGCGATCTTTCACCGCAAGGTTGGAGTAGGCCACGGAGCTCATCTCTTGGTTG\n+GCATCCTCCTTCGCAGGTGAGGTGCCACCCTTGACATCAAGTGCAGGCCTCGACGTTGTT\n+GGCATTTCAGAGCCTTGGCAGAAGTTGGATAAATTGGCGGGAAGTGATGCTGCCAGCTGG\n+AGCTGTTGTGACGCCGCGGCTTCCTGCAGAGCTGAGCCACATCCAGTACGATGGGGACAA\n+CTTGGGCTCCCGATCCTGACAGACTTGGGTTCGAACCCTCAGGGACCTCGCGCGAGGCGC\n+TTTAGTCAGTTTCTCCATCTCCTCGCCGTCGCCAGTCCTCG\n+>TRINITY_DN18_c0_g1_i1 len=3276 path=[3254:0-3275] [-1, 3254, -2]\n+GGGGGGCTATTTCCTAGGGGCGCCGATCAAGAATACAGTGCATTTCGAGTAGGGATGGTT\n+CAGTTTTCCACTTCGGAGTTCAGACTGACACCCCACATCGACAATTTGGAGGTGGCAAAC\n+AGCTTCGCAGTCACTAATGCTTTCTGCTCCCAGTTTTCGAGAGGAGTCTATGCTATTTTT\n+GGATTTTATGACAAGAAGTCTGTAAATACCATCACATCATTTTGCGGAACACTCCACGTC\n+TCCTTCATCACTCCCAGCTTCCCAACAGATGGCACACATCCATTTGTCATTCAGATGAGA\n+CCCGACCTCAAAGGAGCTCTCCTTAGCTTGATTGAATACTATCAATGGGACAAGTTTGCA\n+TACCTCTATGACAGTGACAGAGGCTTATCAACACTGCAAGCTGTGCTGGATTCTGCTGCT\n+GAAAAGAAATGGCAAGTGACTGCTATCAATGTGGGAAACATTAACAATGACAAGAAAGAT\n+GAGATGTACCGATCACTTTTTCAAGATCTGGAGTTAAAAAAGGAACGGCGTGTAATTCTG\n+GACTGTGAAAGGGATAAAGTAAACGACATTGTAGACCAGGTTATTACCATTGGAAAACAT\n+GTTAAAGGGTACCACTACATCATTGCAAATCTGGGATTTACTGATGGAGACCTATTAAAA\n+ATCCAGTTTGGAGGTGCAAATGTCTCTGGATTTCAGATAGTGGACTATGATGATTCGTTG\n+GTATCTAAATTTATAGAAAGATGGTCAACACTGGAAGAAAAAGAATACCCTGGAGCTCAC\n+ACAACAACAATTAAGTATACTTCTGCTCTGACCTATGATGCCGTTCAAGTGATGACTGAA\n+GCCTTCCGCAACCTAAGGAAGCAAAGAATTGAAATCTCCCGAAGGGGGAATGCAGGAGAC\n+TGTCTGGCAAACCCAGCAGTGCCCTGGGGACAAGGTGTAGAAATAGAAAGGGCCCTCAAA\n+CAGGTTCAGGTTGAAGGTCTCTCAGGAAATATAAAGTTTGACCAGAATGGAAAAAGAATA\n+AACTATACAATTAACATCATGGAGCTCAAAACTAATGGGCCCCGGAAGATTGGCTACTGG\n+AGTGAAGTGGACAAAATGGTTGTTACCCTTACTGAGCTCCCTTCTGGAAATGACACCTCT\n+GGGCTTGAGAATAAGACTGTTGTTGTCACCACAATTTTGGAATCTCCGTATGTTATGATG\n+AAGAAAAATCATGAAATGCTTGAAGGCAATGAGCGCTATGAGGGCTACTGTGTTGACCTG\n+GCTGCAGAAATCGCCAAACATTGTGGGTTCAAGTACAAGTTGACAATTGTTGGTGATGGC\n+AAGTATGGGGCCAGGGATGCAGACACGAAAATTTGGAATGGGATGGTTGGAGAACTTGTA\n+TATGGGAAAGCTGATATTGCAATTGCTCCATTAACTATTACCCTTGTGAGAGAAGAGGTG\n+ATTGACTTCTCAAAGCCCTTCATGAGCCTCGGGATATCTATCATGATCAAGAAGCCTCAG\n+AAGTCCAAACCAGGAGTGTTTTCCTTTCTTGATCCTTTAGCCTATGAGATCTGGATGTGC\n+ATTGTTTTTGCCTACATTGGGGTCAGTGTAGTTTTATTCCTGGTCAGCAGATTTAGCCCC\n+TACGAGTGGCACACTGAGGAGTTTGAAGATGGAAGAGAAACACAAAGTAGTGAATCAACT\n+AATGAATTTGGGATTTTTAATAGTCTCTGGTTTTCCTTGGGTGCCTTTATGCAGCAAGGA\n+TGCGATATTTCGCCAAGATCCCTCTCTGGGCGCATTGTTGGAGGTGTGTGGTGGTTCTTT\n+ACCCTGATCATAATCTCCTCCTACACGGCTAACTTAGCTGCCTTCCTGACTGTAGAGAGG\n+ATGGTGTCTCCCATCGAAAGTGCTGAGGATCTTTCTAAGCAAACAGAAATTGCTTATGGA\n+ACATTAGACTCTGGCTCCACTAAAGAGTTTTTCAGGAGATCTAAAATTGCAGTGTTTGAT\n+AAAATGTGGACCTACATGCGGAGTGCGGAGCCCTCTGTGTTTGTGAGGACTACGGCCGAA\n+GGGGTGGCTAGAGTGCGGAAGTCCAAAGGGAAATATGCCTACTTGTTGGAGTCCACGATG\n+AACGAGTACATTGAGCAAAGGAAGCCTTGCGACACCATGAAAGTTGGTGGAAACCTGGAT\n+TCCAAAGGCTATGGCATCGCAACACCTAAAGGATCCTCATTAAGAACCCCAGTAAATCTT\n+GCAGTATTGAAACTCAGTGAGCAAGGCGTCTTAGACAAGCTGAAAAACAAATGGTGGTAC\n+GATAAAGGTGAATGTGGAGCCAAGGACTCTGGAAGTA'..b'GC\n+ACCGAGTGCCCGCAGGTCGTGGATGGTGAAGGGCCAGAGGTGGAGCACGTTGTGGCGAGA\n+GAACTTGGTGCGCTTTTCCACCAGCACCACTCGGGCCCCCAGCAGCGCCAGCTCCACAGC\n+GACCCGCAGCCCGCAAGGTCCAGCACCCACCACCAGGCACTTGGTGCTGGTGCAGGCCCG\n+GCCCTGCTGGTAGACAGGCTGGCCTGCTCGCTTGTCCAGCTTGGTCCACAGTGACTTGGC\n+GCTCCAGTAGTTGAGCTGGTCCTTGATCTTGTGGTACTGGGGCAGCCCCCCACCGGGTTC\n+CAGCCCCAGGGCCCCACACAGCTCCTGGAAGCTGCTCAGCACGTCCTGGCACAGCTGGGC\n+CTGCAGGAAGCTCTCAAAGTGGGCATGCGCTGGGTTGGTGGAGGTAGGTGAAGCCATGGA\n+GGCCTCCTGGGGAGGGCAGCAGCTGGGCAGAGATGAGTGGCGGCGGCTCCGAAGCCGGGA\n+GGGGCCGCTTCCTGTTGGGCTGGCAACCAGGTCTGAGCGGGTGGGAGGGCGGGGGCGGGG\n+GCGGGGGCGGAAACGCCGAGATCGGGCGGGGATGCTGGGATGCGGGGCGGCCCGGGGCGT\n+GCGCCTGGAGTCGCGCGGAGTGTGGGCTTCCGCGAGGGGCGCGGGGCGCCGCCCGGGCTT\n+TATTCGCGACTCATTAGCATCTCATTACTTCTGGATCCCTCTACCGCCTCCAGCGGGGAC\n+AGTCTTGG\n+>TRINITY_DN4_c0_g1_i1 len=3072 path=[3050:0-3071] [-1, 3050, -2]\n+AAAGATCCCCAGGTTATTTTATTGCTGTACTCAGAGGTCAGTTAATGCCCCCGGCCGCCT\n+CACCCTCCCCCCGGCGGTGGCTGAGTCCTCTGCTAGGGTTCGCGAACGGCAGCGGGTCCG\n+AGGGTCACCTCTGCATCTCGCCGCCGGAGGCGCCCCCGCCTCCCCTCCCCGCCGCCGGGC\n+CAGCCGGGGTCCGAGGCCCGCAGCCCCCGGCTGGGAAGGCAGGTCTGGAGAGGCCGCTCC\n+GGGTCTGGAGGGAGGGGAGGCTCTCCGGAAAGGGGTGGCGAGAGACCCCCGCCACGACTC\n+CCAAGCTTCTTCGCGCGCGCTGGAGGGGACACGGTGGGCGCCTAATTCTCGGCGTAGCAG\n+TAGGTCCCATAGGCTGCCTGTTGGGGCCTGGGGAAGCCGAAACTGCGCACTCCGGGATCC\n+GGGAGCCCCCCGCAGCGCGGCCTCGGCGTGGTGATTGGGAAGCGCACACTGCCGTCAGCC\n+AGCCAGCCGCCGTCGCACTGGTCTAGCCCCGAAAACTTCCAGGCGGCGTAGAGGTGCCCA\n+ACCTTGGCCACCACGGCGCCGCGTCGCCGGCACGCCGCGTGGGCTTCAGACAGCGTCAGC\n+CGCCCGGGCACGAAGAACACTTGGCCCGCCAGCGCGGAGGTGAAGCAGAAGGCGTCGTAG\n+CGGTCGCGCATCCGGTCGCGGGGTCCGTAGCTGCGGATCCCGGGCCGGCCTCGGCCGCCG\n+CACGGGGCGCGTGCGGTGAGCACAGGGTAGCGCACGGAGCCCTCGAGCAGCCAGCCCGCG\n+TTACACCAGTCCAGACCCTCGGTCCAAGCCTGGTAGAGCTGGGAGTAGGTGGCCAGGCGT\n+CCGTCCTGCTCCTCGCACGCCTGCTTCGCCTCGTAGTAATTGAACTGGTACCGGCCCCGG\n+CTGGGTTGGTACGGAAACACCACACCCTCCAAGCTCAAGGTCAGCGCCACGCTCTCGTCC\n+TCGATGCCGTTGATGAGCTCGCAGCGGTACCGGCCCTCGTCCTCCAGGCGCACGCCCGCG\n+ATGACCAGGGAGGCGTCTAGTCGATGCCCCCTCCGCATCCTGGCGCGCCCTCCCAGGGGC\n+CCATACCCCCGGGCGTGCAGTCCGTTGGTGATGAGGATCAGCGTTTCCCGGAGCTCCCCA\n+GGCTCCACCTTGCTCCAGCGCACCTTGTAGCTGGGAGGCGTGGTGCCCAGGACGCAGGGC\n+AGCGTGGCCGTGGCCCCACGATGAGAGTGAATGACCTCGTGGATGGGGGGCAGGAGGTAG\n+TGGGGGCCCGGGTGGGATGCTGGGTCTCCTTGGGCTTTGTGGAAGATGGTGAAGGCCCAA\n+AGAAGGAAGCGGCAGAGTGTGGGGAGGGTGAGCCAGCCTGGCATGATGGGGGGTCAGCCC\n+GGCACCGTTTTTGGAATTCCCACTCTCTGTTGTCCAATGGACACACCTGTCGTGTTTTGA\n+GCCAGCGAGAGATGCAGTGGAAGTGAAAAGCATGCTGAAAGAAAACATATATTTTATTAA\n+AAATAACTCTATGCAGGCTCAGCCATCGAGCGACAACAGGTCCCACAGGGTAGTGGCATG\n+GGTGACATATAGTGGGCAAGAAAAGAAAAGAAGACAACGAGAGGCAAAAGTTCAACAACT\n+GATTATATCTTGGTTAGATGCAAGGGTATTTCCAACAAAGCATTTGTTAGAAATGTCATT\n+ACTACTAAAGGAAATCATTCAGGAAGCACAGGAGTATGTGCCAGCACTGAGCTCTCTTCT\n+ATTTAAGAGAACGTGGAATGTGGCTCCTTGGTCCCATTCAGCCTGTAAGGGGATACTTCC\n+ACTTTCTTTGGGAAAGGAGGCCCCTCATCAATGCAGATTTCAAATATCCCCATTCTGGGT\n+CTCTAGCTTCCCTCCCACCCTCCTGCCCCTGGAGAATGCGACCTGTAGGAGCAGAGCCTT\n+CTCCCCAGCCCTTGGTAGAGAAGTGCATGGTCACTGCCGCCCACCCAGAACTGAGACGGG\n+CACTTCCCCAACCTCCCCACACCCAGCTCAGCTCTGGTCAAAGAAACTTTATTTCTAGAT\n+TTATTCACAGACATATTGATATTACAAGAGCTCAGTACTTCACGTGCCTTTAATGGGTGA\n+GGGACTTTGTCTTAGGGAATGAGATAAAAGAAAATTGGGGTAAAAGGAAGTATTCTTATG\n+AGGGACAAACGGCACACAAGCAGCCTAAAGAGCATCAAAAGGCTTATTTCATAATCAAGA\n+CAAGAAGTAAAAAGACAAGAGTATCAAGAACACTGGTAACTGACAGGGAGCTAGAAGTCT\n+GCTTAGATTTGGGAAAAGGACAATCTGCATGCAGTTTTTTGGCGTGGGCTCATGACATGC\n+AGATGCTAATCACAATGCTTCTGCAATGAGCACTTCTCCCCCTGCTCATGTGCGTATTAG\n+GACAGACGCAGCAAGTGCTTCCTTCATTTCGTCTGTGATTGGTGCACTGTGGTGGGGCAC\n+GGGCAGAAATTACTCACCCTAACAAAACAACAAAAGCTTTACAAGCTTCATTTAATAACA\n+ACTGAAATCTGGTCGGTACGTCTCCCAAAGTATGTATGGAACTTAAGGGATTATATAATA\n+TGGATTATTATCTTGTGAAATGTTTTTTGACAAAGACAAAAATATAATTCAGTAACTAAG\n+AGTGGAATCCACAGCTAGTACACTAGGGATACCCAAGAGGACAAATATTCTCTTAGAGTG\n+ACAGCCTTTTGGAAGATCCCTTTTCAGCTGACTCTTGTATAACTCACTGTGAAAAAGAGA\n+AAGAGCAAAATTTCCAAAAGGCAGAAAGCAGAGACATTTTTCTTAACCATCAGGTGTTGG\n+GGTCGGGCTCACCGAAGGGTATTCGACAGCTTCTCCCTCTCCCACCTCACCCACTGAGCA\n+CTTTGCAGCAGTACGGTGTCCTGGTAGAGCCCAACTAAGTCAGAGCATACCACGCGCTGG\n+GGAAAAGGGGGCTGTAAAGGAGGTGTCAGGGAGGTGACAGCACCCCTGAACATTTACTAA\n+GATGTATTAATGGATATATTTAGCGGTCAAAGTACAATTTACAGAAGATAAATTTATAGT\n+ACTTGACAGTTT\n' 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