Mercurial > repos > iuc > samtools_fastx
changeset 2:720217c23995 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:13:01 +0000 |
| parents | a8d69aee190e |
| children | b3d99709fe1a |
| files | macros.xml samtools_fastx.xml test-data/11.1.fq.expected test-data/11.2.fq.expected test-data/11.s.fq.expected test-data/7.1.fq.expected test-data/7.2.fq.expected test-data/7.s.fq.expected test-data/8.1.fq.expected test-data/8.2.fq.expected test-data/8.i.fq.expected test-data/8.s.fq.expected test-data/bc.fq.expected test-data/bc10.fq.expected |
| diffstat | 14 files changed, 324 insertions(+), 131 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Fri Sep 28 04:39:19 2018 -0400 +++ b/macros.xml Tue Sep 28 16:13:01 2021 +0000 @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> - <xml name="flag_options"> - <option value="1">read is paired</option> - <option value="2">read is mapped in a proper pair</option> - <option value="4">read is unmapped</option> - <option value="8">mate is unmapped</option> - <option value="16">read reverse strand</option> - <option value="32">mate reverse strand</option> - <option value="64">read is the first in a pair</option> - <option value="128">read is the second in a pair</option> - <option value="256">alignment or read is not primary</option> - <option value="512">read fails platform/vendor quality checks</option> - <option value="1024">read is a PCR or optical duplicate</option> - <option value="2048">supplementary alignment</option> + <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab':
--- a/samtools_fastx.xml Fri Sep 28 04:39:19 2018 -0400 +++ b/samtools_fastx.xml Tue Sep 28 16:13:01 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy1"> +<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>extract FASTA or FASTQ from alignment files</description> <macros> <import>macros.xml</import> @@ -7,10 +7,10 @@ <expand macro="stdio"/> <expand macro="version_command" /> <command><![CDATA[ -@ADDTHREADS@ +@ADDTHREADS@ ## name sort input file if neccessary #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'): - samtools sort -@ \$addthreads -n '$input' > input && + samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input && #else: ln -s '$input' input && #end if @@ -39,21 +39,15 @@ #if 'r2' in str($outputs): -2 reverse.$output_fmt_cond.output_fmt_select #end if -#if str($inclusive_filter) != 'None': - #set $filter = $inclusive_filter - @FLAGS@ - -f $flags -#end if -#if str($exclusive_filter) != 'None': - #set $filter = $exclusive_filter - @FLAGS@ - -F $flags -#end if -#if str($exclusive_filter) != 'None': - #set $filter = $exclusive_filter_all - @FLAGS@ - -G $flags -#end if +#set $filter = $inclusive_filter +@FLAGS@ +-f $flags +#set $filter = $exclusive_filter +@FLAGS@ +-F $flags +#set $filter = $exclusive_filter_all +@FLAGS@ +-G $flags #if 's' in str($outputs): -s singletons.$output_fmt_cond.output_fmt_select #end if @@ -75,12 +69,12 @@ #end if #end if -input +input #if str($outputs)=='None' or 'other' in str($outputs): ## since currently stdout in not zipped (samtools doesn't know about the extension) #if str($output_fmt_cond.output_fmt_select).endswith('.gz'): - | gzip - + | gzip - #end if > output.$output_fmt_cond.output_fmt_select && ln -s output.$output_fmt_cond.output_fmt_select output @@ -148,10 +142,10 @@ <option value="-N">always append /1 and /2 to read name</option> </param> <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> - <expand macro="flag_options" /> + <expand macro="flag_options"/> </param> <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set"> - <expand macro="flag_options" /> + <expand macro="flag_options" s256="true" s2048="true"/> </param> <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> <expand macro="flag_options" /> @@ -270,8 +264,8 @@ <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" /> <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" /> </test> - <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used - for compressing stdout does not give exactly the same file contents .. the other + <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used + for compressing stdout does not give exactly the same file contents .. the other compressed files seem to)--> <test> <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> @@ -279,7 +273,7 @@ <param name="output_fmt_select" value="fasta.gz" /> </conditional> <param name="outputs" value="other" /> - <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" compare="sim_size" /> + <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/> </test> <test> <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> @@ -287,9 +281,9 @@ <param name="output_fmt_select" value="fastqsanger.gz" /> </conditional> <param name="outputs" value="r0,r1,r2" /> - <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" /> - <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" /> - <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" /> + <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> + <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> + <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> </test> <test> <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> @@ -297,9 +291,9 @@ <param name="output_fmt_select" value="fasta.gz" /> </conditional> <param name="outputs" value="r0,r1,r2" /> - <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" /> - <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" /> - <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" /> + <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" decompress="true" /> + <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" decompress="true" /> + <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" /> </test> <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313--> <!--# basic 2 output test without singleton tracking--> @@ -476,12 +470,16 @@ <param name="ilumina_casava" value="-i" /> </conditional> <param name="outputs" value="r1,r2,s,other" /> + <conditional name="idxout_cond"> + <param name="idxout_select" value="yes"/> + <param name="index_format" value="n2i2"/> + </conditional> <param name="copy_tags" value="-t" /> <param name="copy_arb_tags" value="MD,ia" /> <param name="read_numbering" value="-N"/> - <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" /> - <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" /> - <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" /> + <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" /> + <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" /> + <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" /> <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> </test> <!--# -i flag with index-->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.1.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -0,0 +1,68 @@ +@ref1_grp1_p001/1 1:N:0:AC+GT MD:Z:10 RG:Z:grp1 BC:Z:AC-GT +CGAGCTCGGT ++ +!!!!!!!!!! +@ref1_grp1_p002/1 1:N:0:AATT+CCGG MD:Z:10 RG:Z:grp1 BC:Z:AATT+CCGG +CTCGGTACCC ++ +########## +@ref1_grp1_p003/1 1:N:0:0 MD:Z:10 RG:Z:grp1 +GTACCCGGGG ++ +%%%%%%%%%% +@ref1_grp1_p004/1 1:N:0:0 MD:Z:10 RG:Z:grp1 +CCGGGGATCC ++ +'''''''''' +@ref1_grp1_p005/1 1:N:0:0 MD:Z:10 RG:Z:grp1 ia:i:40000 +GGATCCTCTA ++ +)))))))))) +@ref1_grp1_p006/1 1:N:0:0 MD:Z:10 RG:Z:grp1 ia:i:255 +CCTCTAGAGT ++ +++++++++++ +@ref1_grp2_p001/1 1:N:0:TG+CA MD:Z:8 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd +AGCTCGGTAC ++ +"""""""""" +@ref1_grp2_p002/1 1:N:0:0 MD:Z:10 RG:Z:grp2 +CGGTACCCGG ++ +$$$$$$$$$$ +@ref1_grp2_p003/1 1:N:0:0 MD:Z:10 RG:Z:grp2 ia:i:4294967295 +ACCCGGGGAT ++ +&&&&&&&&&& +@ref1_grp2_p004/1 1:N:0:0 MD:Z:10 RG:Z:grp2 ia:i:-2147483648 +GGGGATCCTC ++ +(((((((((( +@ref1_grp2_p005/1 1:N:0:0 MD:Z:10 RG:Z:grp2 ia:i:-1000 +ATCCTCTAGA ++ +********** +@ref1_grp2_p006/1 1:N:0:0 MD:Z:10 RG:Z:grp2 ia:i:-1 +TCTAGAGTCG ++ +,,,,,,,,,, +@ref2_grp3_p001/1 1:N:0:0 MD:Z:15 RG:Z:grp3 +GTGACACTATAGAAT ++ +~~~~~~~~~~~~~~~ +@ref2_grp3_p002/1 1:N:0:0 MD:Z:15 RG:Z:grp3 +CTGTTTCCTGTGTGA ++ +{{{{{{{{{{{{{{{ +@ref2_grp3_p003/1 1:N:0:0 MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 RG:Z:grp3 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/1 1:N:0:0 MD:Z:10 RG:Z:grp1 +TGCAGGCATG ++ +AAAAAAAAAA +@ref12_grp2_p001/1 1:N:0:0 MD:Z:10 RG:Z:grp2 +CAAGCTTGAG ++ +AAAAAAAAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.2.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -0,0 +1,68 @@ +@ref1_grp1_p001/2 2:N:0:AC+GT MD:Z:10 RG:Z:grp1 BC:Z:AC-GT +GTCGACTCTA ++ +---------- +@ref1_grp1_p002/2 2:N:0:AATT+CCGG MD:Z:10 RG:Z:grp1 BC:Z:AATT+CCGG +GCAGGTCGAC ++ +////////// +@ref1_grp1_p003/2 2:N:0:0 MD:Z:10 RG:Z:grp1 +GCCTGCAGGT ++ +1111111111 +@ref1_grp1_p004/2 2:N:0:0 MD:Z:10 RG:Z:grp1 +GCATGCCTGC ++ +3333333333 +@ref1_grp1_p005/2 2:N:0:0 MD:Z:10 RG:Z:grp1 +GCTTGCATGC ++ +5555555555 +@ref1_grp1_p006/2 2:N:0:0 MD:Z:10 RG:Z:grp1 +TCAAGCTTGC ++ +7777777777 +@ref1_grp2_p001/2 2:N:0:TG+CA MD:Z:10 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd +AGGTCGACTC ++ +.......... +@ref1_grp2_p002/2 2:N:0:0 MD:Z:10 RG:Z:grp2 +CTGCAGGTCG ++ +0000000000 +@ref1_grp2_p003/2 2:N:0:0 MD:Z:10 RG:Z:grp2 +ATGCCTGCAG ++ +2222222222 +@ref1_grp2_p004/2 2:N:0:0 MD:Z:10 RG:Z:grp2 +TTGCATGCCT ++ +4444444444 +@ref1_grp2_p005/2 2:N:0:0 MD:Z:10 RG:Z:grp2 +AAGCTTGCAT ++ +6666666666 +@ref1_grp2_p006/2 2:N:0:0 MD:Z:10 RG:Z:grp2 +ACTCAAGCTT ++ +8888888888 +@ref2_grp3_p001/2 2:N:0:0 MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 RG:Z:grp3 +CTGTTTCCTGTGTGA ++ +||||||||||||||| +@ref2_grp3_p002/2 2:N:0:0 MD:Z:15 RG:Z:grp3 +CGCCAAGCTATTTAG ++ +}}}}}}}}}}}}}}} +@ref2_grp3_p003/2 2:N:0:0 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 RG:Z:grp3 +ACGTMRWSYKVHDBN ++ +0123456789abcd! +@ref12_grp1_p001/2 2:N:0:0 MD:Z:10 RG:Z:grp1 +CACTATAGAA ++ +BBBBBBBBBB +@ref12_grp2_p001/2 2:N:0:0 MD:Z:10 RG:Z:grp2 +ATTTAGGTGA ++ +BBBBBBBBBB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.s.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -0,0 +1,8 @@ +@ref1_grp2_p002a/1 1:N:0:0 MD:Z:10 RG:Z:grp2 +CGGTACCCGG ++ +$$$$$$$$$$ +@unaligned_grp3_p001/1 1:N:0:0 RG:Z:grp3 +CACTCGTTCATGACG ++ +0123456789abcde
--- a/test-data/7.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/7.1.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,68 +1,68 @@ -@ref1_grp1_p001/1 RG:Z:grp1 BC:Z:AC-GT MD:Z:10 +@ref1_grp1_p001/1 MD:Z:10 RG:Z:grp1 BC:Z:AC-GT CGAGCTCGGT + !!!!!!!!!! -@ref1_grp1_p002/1 RG:Z:grp1 BC:Z:AATT+CCGG MD:Z:10 +@ref1_grp1_p002/1 MD:Z:10 RG:Z:grp1 BC:Z:AATT+CCGG CTCGGTACCC + ########## -@ref1_grp1_p003/1 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p003/1 MD:Z:10 RG:Z:grp1 GTACCCGGGG + %%%%%%%%%% -@ref1_grp1_p004/1 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p004/1 MD:Z:10 RG:Z:grp1 CCGGGGATCC + '''''''''' -@ref1_grp1_p005/1 RG:Z:grp1 MD:Z:10 ia:i:40000 +@ref1_grp1_p005/1 MD:Z:10 RG:Z:grp1 ia:i:40000 GGATCCTCTA + )))))))))) -@ref1_grp1_p006/1 RG:Z:grp1 MD:Z:10 ia:i:255 +@ref1_grp1_p006/1 MD:Z:10 RG:Z:grp1 ia:i:255 CCTCTAGAGT + ++++++++++ -@ref1_grp2_p001/1 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd MD:Z:8 +@ref1_grp2_p001/1 MD:Z:8 RG:Z:grp2 BC:Z:TG+CA QT:Z:ab+cd AGCTCGGTAC + """""""""" -@ref1_grp2_p002/1 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p002/1 MD:Z:10 RG:Z:grp2 CGGTACCCGG + $$$$$$$$$$ -@ref1_grp2_p003/1 RG:Z:grp2 MD:Z:10 ia:i:4294967295 +@ref1_grp2_p003/1 MD:Z:10 RG:Z:grp2 ia:i:4294967295 ACCCGGGGAT + &&&&&&&&&& -@ref1_grp2_p004/1 RG:Z:grp2 MD:Z:10 ia:i:-2147483648 +@ref1_grp2_p004/1 MD:Z:10 RG:Z:grp2 ia:i:-2147483648 GGGGATCCTC + (((((((((( -@ref1_grp2_p005/1 RG:Z:grp2 MD:Z:10 ia:i:-1000 +@ref1_grp2_p005/1 MD:Z:10 RG:Z:grp2 ia:i:-1000 ATCCTCTAGA + ********** -@ref1_grp2_p006/1 RG:Z:grp2 MD:Z:10 ia:i:-1 +@ref1_grp2_p006/1 MD:Z:10 RG:Z:grp2 ia:i:-1 TCTAGAGTCG + ,,,,,,,,,, -@ref2_grp3_p001/1 RG:Z:grp3 MD:Z:15 +@ref2_grp3_p001/1 MD:Z:15 RG:Z:grp3 GTGACACTATAGAAT + ~~~~~~~~~~~~~~~ -@ref2_grp3_p002/1 RG:Z:grp3 MD:Z:15 +@ref2_grp3_p002/1 MD:Z:15 RG:Z:grp3 CTGTTTCCTGTGTGA + {{{{{{{{{{{{{{{ -@ref2_grp3_p003/1 RG:Z:grp3 MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 +@ref2_grp3_p003/1 MD:Z:1T0T0C0T0A0T0A0G0T0G0T0C0A0C0 RG:Z:grp3 ACGTMRWSYKVHDBN + 0123456789abcd! -@ref12_grp1_p001/1 RG:Z:grp1 MD:Z:10 +@ref12_grp1_p001/1 MD:Z:10 RG:Z:grp1 TGCAGGCATG + AAAAAAAAAA -@ref12_grp2_p001/1 RG:Z:grp2 MD:Z:10 +@ref12_grp2_p001/1 MD:Z:10 RG:Z:grp2 CAAGCTTGAG + AAAAAAAAAA
--- a/test-data/7.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/7.2.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,68 +1,68 @@ -@ref1_grp1_p001/2 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p001/2 MD:Z:10 RG:Z:grp1 GTCGACTCTA + ---------- -@ref1_grp1_p002/2 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p002/2 MD:Z:10 RG:Z:grp1 GCAGGTCGAC + ////////// -@ref1_grp1_p003/2 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p003/2 MD:Z:10 RG:Z:grp1 GCCTGCAGGT + 1111111111 -@ref1_grp1_p004/2 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p004/2 MD:Z:10 RG:Z:grp1 GCATGCCTGC + 3333333333 -@ref1_grp1_p005/2 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p005/2 MD:Z:10 RG:Z:grp1 GCTTGCATGC + 5555555555 -@ref1_grp1_p006/2 RG:Z:grp1 MD:Z:10 +@ref1_grp1_p006/2 MD:Z:10 RG:Z:grp1 TCAAGCTTGC + 7777777777 -@ref1_grp2_p001/2 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p001/2 MD:Z:10 RG:Z:grp2 AGGTCGACTC + .......... -@ref1_grp2_p002/2 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p002/2 MD:Z:10 RG:Z:grp2 CTGCAGGTCG + 0000000000 -@ref1_grp2_p003/2 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p003/2 MD:Z:10 RG:Z:grp2 ATGCCTGCAG + 2222222222 -@ref1_grp2_p004/2 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p004/2 MD:Z:10 RG:Z:grp2 TTGCATGCCT + 4444444444 -@ref1_grp2_p005/2 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p005/2 MD:Z:10 RG:Z:grp2 AAGCTTGCAT + 6666666666 -@ref1_grp2_p006/2 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p006/2 MD:Z:10 RG:Z:grp2 ACTCAAGCTT + 8888888888 -@ref2_grp3_p001/2 RG:Z:grp3 MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 +@ref2_grp3_p001/2 MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 RG:Z:grp3 CTGTTTCCTGTGTGA + ||||||||||||||| -@ref2_grp3_p002/2 RG:Z:grp3 MD:Z:15 +@ref2_grp3_p002/2 MD:Z:15 RG:Z:grp3 CGCCAAGCTATTTAG + }}}}}}}}}}}}}}} -@ref2_grp3_p003/2 RG:Z:grp3 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 +@ref2_grp3_p003/2 MD:Z:0A0T0T0C0T0A0T0A0G0T0G0T1A0C0 RG:Z:grp3 ACGTMRWSYKVHDBN + 0123456789abcd! -@ref12_grp1_p001/2 RG:Z:grp1 MD:Z:10 +@ref12_grp1_p001/2 MD:Z:10 RG:Z:grp1 CACTATAGAA + BBBBBBBBBB -@ref12_grp2_p001/2 RG:Z:grp2 MD:Z:10 +@ref12_grp2_p001/2 MD:Z:10 RG:Z:grp2 ATTTAGGTGA + BBBBBBBBBB
--- a/test-data/7.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/7.s.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,4 +1,4 @@ -@ref1_grp2_p002a/1 RG:Z:grp2 MD:Z:10 +@ref1_grp2_p002a/1 MD:Z:10 RG:Z:grp2 CGGTACCCGG + $$$$$$$$$$
--- a/test-data/8.1.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/8.1.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,68 +1,68 @@ -@ref1_grp1_p001 1:N:0:GT +@ref1_grp1_p001 1:N:0:ACGT CGAGCTCGGT + !!!!!!!!!! -@ref1_grp1_p002 1:N:0:TT +@ref1_grp1_p002 1:N:0:AATTCCGG CTCGGTACCC + ########## -@ref1_grp1_p003 +@ref1_grp1_p003 1:N:0:0 GTACCCGGGG + %%%%%%%%%% -@ref1_grp1_p004 +@ref1_grp1_p004 1:N:0:0 CCGGGGATCC + '''''''''' -@ref1_grp1_p005 +@ref1_grp1_p005 1:N:0:0 GGATCCTCTA + )))))))))) -@ref1_grp1_p006 +@ref1_grp1_p006 1:N:0:0 CCTCTAGAGT + ++++++++++ -@ref1_grp2_p001 1:N:0:CA +@ref1_grp2_p001 1:N:0:TGCA AGCTCGGTAC + """""""""" -@ref1_grp2_p002 +@ref1_grp2_p002 1:N:0:0 CGGTACCCGG + $$$$$$$$$$ -@ref1_grp2_p003 +@ref1_grp2_p003 1:N:0:0 ACCCGGGGAT + &&&&&&&&&& -@ref1_grp2_p004 +@ref1_grp2_p004 1:N:0:0 GGGGATCCTC + (((((((((( -@ref1_grp2_p005 +@ref1_grp2_p005 1:N:0:0 ATCCTCTAGA + ********** -@ref1_grp2_p006 +@ref1_grp2_p006 1:N:0:0 TCTAGAGTCG + ,,,,,,,,,, -@ref2_grp3_p001 +@ref2_grp3_p001 1:N:0:0 GTGACACTATAGAAT + ~~~~~~~~~~~~~~~ -@ref2_grp3_p002 +@ref2_grp3_p002 1:N:0:0 CTGTTTCCTGTGTGA + {{{{{{{{{{{{{{{ -@ref2_grp3_p003 +@ref2_grp3_p003 1:N:0:0 ACGTMRWSYKVHDBN + 0123456789abcd! -@ref12_grp1_p001 +@ref12_grp1_p001 1:N:0:0 TGCAGGCATG + AAAAAAAAAA -@ref12_grp2_p001 +@ref12_grp2_p001 1:N:0:0 CAAGCTTGAG + AAAAAAAAAA
--- a/test-data/8.2.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/8.2.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,68 +1,68 @@ -@ref1_grp1_p001 1:N:0:GT +@ref1_grp1_p001 2:N:0:ACGT GTCGACTCTA + ---------- -@ref1_grp1_p002 1:N:0:TT +@ref1_grp1_p002 2:N:0:AATTCCGG GCAGGTCGAC + ////////// -@ref1_grp1_p003 +@ref1_grp1_p003 2:N:0:0 GCCTGCAGGT + 1111111111 -@ref1_grp1_p004 +@ref1_grp1_p004 2:N:0:0 GCATGCCTGC + 3333333333 -@ref1_grp1_p005 +@ref1_grp1_p005 2:N:0:0 GCTTGCATGC + 5555555555 -@ref1_grp1_p006 +@ref1_grp1_p006 2:N:0:0 TCAAGCTTGC + 7777777777 -@ref1_grp2_p001 1:N:0:CA +@ref1_grp2_p001 2:N:0:TGCA AGGTCGACTC + .......... -@ref1_grp2_p002 +@ref1_grp2_p002 2:N:0:0 CTGCAGGTCG + 0000000000 -@ref1_grp2_p003 +@ref1_grp2_p003 2:N:0:0 ATGCCTGCAG + 2222222222 -@ref1_grp2_p004 +@ref1_grp2_p004 2:N:0:0 TTGCATGCCT + 4444444444 -@ref1_grp2_p005 +@ref1_grp2_p005 2:N:0:0 AAGCTTGCAT + 6666666666 -@ref1_grp2_p006 +@ref1_grp2_p006 2:N:0:0 ACTCAAGCTT + 8888888888 -@ref2_grp3_p001 +@ref2_grp3_p001 2:N:0:0 CTGTTTCCTGTGTGA + ||||||||||||||| -@ref2_grp3_p002 +@ref2_grp3_p002 2:N:0:0 CGCCAAGCTATTTAG + }}}}}}}}}}}}}}} -@ref2_grp3_p003 +@ref2_grp3_p003 2:N:0:0 ACGTMRWSYKVHDBN + 0123456789abcd! -@ref12_grp1_p001 +@ref12_grp1_p001 2:N:0:0 CACTATAGAA + BBBBBBBBBB -@ref12_grp2_p001 +@ref12_grp2_p001 2:N:0:0 ATTTAGGTGA + BBBBBBBBBB
--- a/test-data/8.i.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/8.i.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,12 +1,12 @@ -@ref1_grp1_p001 1:N:0:GT +@ref1_grp1_p001 1:N:0:ACGT GT + "" -@ref1_grp1_p002 1:N:0:TT +@ref1_grp1_p002 1:N:0:AATTCCGG TT + "" -@ref1_grp2_p001 1:N:0:CA +@ref1_grp2_p001 1:N:0:TGCA CA + -cd +""
--- a/test-data/8.s.fq.expected Fri Sep 28 04:39:19 2018 -0400 +++ b/test-data/8.s.fq.expected Tue Sep 28 16:13:01 2021 +0000 @@ -1,8 +1,8 @@ -@ref1_grp2_p002a +@ref1_grp2_p002a 1:N:0:0 CGGTACCCGG + $$$$$$$$$$ -@unaligned_grp3_p001 +@unaligned_grp3_p001 1:N:0:0 CACTCGTTCATGACG + 0123456789abcde