Mercurial > repos > scisjnu123 > test
changeset 32:bf54a6f75296 draft
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/bam_to_sam.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,54 @@ +<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="version_command"></expand> + <expand macro="stdio"></expand> + <description>convert BAM to SAM</description> + <command> +<![CDATA[ + samtools view -o "${output1}" ${header} "${input1}" +]]> + </command> + <inputs> + <param format="bam" label="BAM File to Convert" name="input1" type="data" /> + <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> + <option value="-h">Include header in SAM output (-h)</option> + <option value="-H">Print header only (-H)</option> + <option value="">Exclude header</option> + </param> + </inputs> + <outputs> + <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" /> + </outputs> + <tests> + <test> + <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> + <param name="header" value="-h" /> + <output file="bam_to_sam_out1.sam" name="output1" sorted="True" /> + </test> + <test> + <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> + <param name="header" value="-H" /> + <output file="bam_to_sam_out2.sam" name="output1" sorted="True" /> + </test> + <test> + <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> + <param name="header" value="" /> + <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +Converts BAM dataset to SAM using ``samtools view`` command:: + + samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] + +]]> + </help> + <expand macro="citations"></expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/test-data/bam_to_sam_in1.sam Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/test-data/bam_to_sam_in2.sam Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,25 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:rg1 SM:s1 +@RG ID:rg2 SM:s3 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/test-data/bam_to_sam_out1.sam Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/test-data/bam_to_sam_out2.sam Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/test-data/bam_to_sam_out3.sam Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,8 @@ +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/bam_to_sam/af7c50162f0b/bam_to_sam/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/README Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1 @@ +TODO
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,87 @@ +#!/usr/bin/env python +#Dan Blankenberg + +import json +import optparse +import os +import subprocess +import sys +import tempfile + +CHUNK_SIZE = 2**20 + +DEFAULT_DATA_TABLE_NAME = "fasta_indexes" + +def get_id_name( params, dbkey, fasta_description=None): + #TODO: ensure sequence_id is unique and does not already appear in location file + sequence_id = params['param_dict']['sequence_id'] + if not sequence_id: + sequence_id = dbkey + + sequence_name = params['param_dict']['sequence_name'] + if not sequence_name: + sequence_name = fasta_description + if not sequence_name: + sequence_name = dbkey + return sequence_id, sequence_name + +def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): + #TODO: allow multiple FASTA input files + assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename + fasta_base_name = os.path.split( fasta_filename )[-1] + sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) + os.symlink( fasta_filename, sym_linked_fasta_filename ) + + args = [ 'samtools', 'faidx' ] + args.append( sym_linked_fasta_filename ) + tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" ) + proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) + return_code = proc.wait() + if return_code: + tmp_stderr.flush() + tmp_stderr.seek( 0 ) + sys.stderr.write( "Error building index:\n" ) + while True: + chunk = tmp_stderr.read( CHUNK_SIZE ) + if not chunk: + break + sys.stderr.write( chunk ) + sys.exit( return_code ) + tmp_stderr.close() + data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) + _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) + +def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): + data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) + data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) + data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) + return data_manager_dict + +def main(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) + parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) + parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) + parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) + (options, args) = parser.parse_args() + + filename = args[0] + + params = json.loads( open( filename ).read() ) + target_directory = params[ 'output_data' ][0]['extra_files_path'] + os.mkdir( target_directory ) + data_manager_dict = {} + + if options.fasta_dbkey in [ None, '', '?' ]: + raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) + + sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) + + #build the index + build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) + + #save info to json file + open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) + +if __name__ == "__main__": main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,25 @@ +<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.2"> + <description>builder</description> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <command interpreter="python">data_manager_sam_fasta_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "fasta_indexes"</command> + <inputs> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + <param type="text" name="sequence_name" value="" label="Name of sequence" /> + <param type="text" name="sequence_id" value="" label="ID for sequence" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + + <help> + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager_conf.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<data_managers> + + <data_manager tool_file="data_manager/data_manager_sam_fasta_index_builder.xml" id="sam_fasta_index_builder" version="0.0.1"> + <data_table name="fasta_indexes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/sam_indexes/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/sam_indexes/${value}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/all_fasta.loc.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/fasta_indexes.loc.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_data_table_conf.xml.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,12 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_cairo_1_12_14/cd2ed5717e38/package_cairo_1_12_14/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="pixman" version="0.32.4"> + <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="fontconfig" version="2.11.1"> + <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="cairo" version="1.12.14"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/cairo/cairo-1.12.14.tar.bz2</action> + <action type="set_environment_for_install"> + <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.4" /> + </repository> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="freetype" version="2.5.2" /> + </repository> + <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="fontconfig" version="2.11.1" /> + </repository> + </action> + <!-- edit configure and build/configure.ac.warnings to allow compiling cairo on gcc-4.9. Fixed in more recent versions of cairo --> + <action type="shell_command"> + sed -i.bak 's|MAYBE_WARN="$MAYBE_WARN -flto"|MAYBE_WARN="$MAYBE_WARN -flto -ffat-lto-objects -fuse-linker-plugin" |' configure build/configure.ac.warnings + </action> + <action type="autoconf">--enable-quartz=no --enable-quartz-font=no --with-x=no --enable-xcb-shm=no --enable-xlib-xcb=no --enable-xcb=no --enable-gtk-doc=no --enable-gtk-doc-html=no --enable-xlib-xrender=no</action> + <!-- Create an empty cairo-xlib.h file, because R's configure script explicitly includes it even if X is disabled. --> + <action type="shell_command">touch $INSTALL_DIR/include/cairo/cairo-xlib.h</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="CAIRO_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> + <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> + <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> + <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include/cairo</environment_variable> + <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include/cairo</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> + <environment_variable action="set_to" name="CAIRO_CFLAGS">-I$INSTALL_DIR/include/cairo</environment_variable> + <environment_variable action="set_to" name="CAIRO_LIBS">"-L$INSTALL_DIR/lib -lcairo"</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_freetype_2_5_2/a65217367e4a/package_freetype_2_5_2/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://download.savannah.gnu.org/releases/freetype/freetype-2.5.2.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + </action> + <action type="autoconf" /> + <action type="set_environment"> + <environment_variable action="set_to" name="FREETYPE_LIB_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include/freetype2</environment_variable> + <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include/freetype2</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libpng" version="1.6.7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.7/libpng-1.6.7.tar.gz</action> + <action type="autoconf"/> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="LIBPNG_ROOT">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="set_to" name="LIBPNG_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + </install> + <readme /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_ncurses_5_9/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,41 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url" sha256sum="9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> + <action type="download_file" sha256sum="c9033021022979a02621af43883e6ca5a4df14d2c3a5a821e4c67923d13d5e78">https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch</action> + <action type="shell_command"> + patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch + </action> + <action type="autoconf">--with-shared --enable-symlinks</action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" sha256sum="9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> + <action type="download_file" sha256sum="c9033021022979a02621af43883e6ca5a4df14d2c3a5a821e4c67923d13d5e78">https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch</action> + <action type="shell_command"> + patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch + </action> + <action type="autoconf">--with-shared --enable-symlinks --without-cxx --without-cxx-binding --without-ada --without-progs --without-curses-h --without-debug --enable-widec --enable-const --enable-ext-colors --enable-sigwinch --enable-wgetch-events</action> + </actions> + <action type="set_environment"> + <environment_variable action="set_to" name="NCURSES_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> + <environment_variable action="set_to" name="NCURSES_LIB_PATH">$INSTALL_DIR/lib/</environment_variable> + <environment_variable action="set_to" name="NCURSES_ROOT_PATH">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> + <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> + <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include/ncurses</environment_variable> + <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include/ncurses</environment_variable> + </action> + </actions_group> + </install> + <readme> + ncurses (new curses) is a programming library that provides an API which allows the programmer + to write text-based user interfaces in a terminal-independent manner + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pixman" version="0.32.4"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action sha256sum="80c7ed420e8a3ae749800241e6347c3d55681296cab71384be7969cd9e657e84" type="download_by_url"> + http://cairographics.org/releases/pixman-0.32.4.tar.gz + </action> + <action type="set_environment_for_install"> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + </action> + <action type="autoconf" /> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="PIXMAN_LIB_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action sha256sum="80c7ed420e8a3ae749800241e6347c3d55681296cab71384be7969cd9e657e84" type="download_by_url"> + http://cairographics.org/releases/pixman-0.32.4.tar.gz + </action> + <action type="set_environment_for_install"> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + </action> + <action type="autoconf">--disable-mmx</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="PIXMAN_LIB_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + </actions_group> + </install> + <readme /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_samtools_0_1_19/95d2c4aefb5f/package_samtools_0_1_19/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,79 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action> + <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bcftools/bcftools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bcftools/vcfutils.pl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>libbam.a</source> + <destination>$INSTALL_DIR/lib</destination> + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/include/bam</destination_directory> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> + <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> +Program: samtools (Tools for alignments in the SAM format) +Version: 0.1.19-44428cd + +Usage: samtools <command> [options] + +Command: view SAM<->BAM conversion + sort sort alignment file + mpileup multi-way pileup + depth compute the depth + faidx index/extract FASTA + tview text alignment viewer + index index alignment + idxstats BAM index stats (r595 or later) + fixmate fix mate information + flagstat simple stats + calmd recalculate MD/NM tags and '=' bases + merge merge sorted alignments + rmdup remove PCR duplicates + reheader replace BAM header + cat concatenate BAMs + bedcov read depth per BED region + targetcut cut fosmid regions (for fosmid pool only) + phase phase heterozygotes + bamshuf shuffle and group alignments by name + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_samtools_1_2/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,81 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> + <action type="set_environment_for_install"> + <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </repository> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </action> + <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> + <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> + <action type="make_install" /> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + </actions> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> +Program: samtools (Tools for alignments in the SAM format) +Version: 1.2 + +Usage: samtools <command> [options] + +Commands: + -- indexing + faidx index/extract FASTA + index index alignment + -- editing + calmd recalculate MD/NM tags and '=' bases + fixmate fix mate information + reheader replace BAM header + rmdup remove PCR duplicates + targetcut cut fosmid regions (for fosmid pool only) + -- file operations + bamshuf shuffle and group alignments by name + cat concatenate BAMs + merge merge sorted alignments + mpileup multi-way pileup + sort sort alignment file + split splits a file by read group + bam2fq converts a BAM to a FASTQ + -- stats + bedcov read depth per BED region + depth compute the depth + flagstat simple stats + idxstats BAM index stats + phase phase heterozygotes + stats generate stats (former bamcheck) + -- viewing + flags explain BAM flags + tview text alignment viewer + view SAM<->BAM<->CRAM conversion + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_zlib_1_2_8/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="zlib" version="1.2.8"> + <install version="1.0"> + <actions> + <action type="download_by_url" sha256sum="36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d">https://depot.galaxyproject.org/software/zlib/zlib_1.2.8_src_all.tar.gz</action> + <action type="autoconf" /> + <action type="set_environment"> + <environment_variable name="ZLIB_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PKG_CONFIG_PATH" action="prepend_to">$INSTALL_DIR/lib/pkgconfig</environment_variable> + <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> + <environment_variable name="LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> + <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> + <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> + </action> + </actions> + </install> + <readme> + A Massively Spiffy Yet Delicately Unobtrusive Compression Library. + http://www.zlib.net/ + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/pileup_interval.py Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,117 @@ +#!/usr/bin/env python + +""" +Condenses pileup format into ranges of bases. + +usage: %prog [options] + -i, --input=i: Input pileup file + -o, --output=o: Output pileup + -c, --coverage=c: Coverage + -f, --format=f: Pileup format + -b, --base=b: Base to select + -s, --seq_column=s: Sequence column + -l, --loc_column=l: Base location column + -r, --base_column=r: Reference base column + -C, --cvrg_column=C: Coverage column +""" + +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse +import sys + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + strout = '' + #Parse Command Line + options, args = doc_optparse.parse( __doc__ ) + coverage = int(options.coverage) + fin = file(options.input, 'r') + fout = file(options.output, 'w') + inLine = fin.readline() + if options.format == 'six': + seqIndex = 0 + locIndex = 1 + baseIndex = 2 + covIndex = 3 + elif options.format == 'ten': + seqIndex = 0 + locIndex = 1 + if options.base == 'first': + baseIndex = 2 + else: + baseIndex = 3 + covIndex = 7 + else: + seqIndex = int(options.seq_column) - 1 + locIndex = int(options.loc_column) - 1 + baseIndex = int(options.base_column) - 1 + covIndex = int(options.cvrg_column) - 1 + lastSeq = '' + lastLoc = -1 + locs = [] + startLoc = -1 + bases = [] + while inLine.strip() != '': + lineParts = inLine.split('\t') + try: + seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex]) + except IndexError, ei: + if options.format == 'ten': + stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) ) + else: + stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) ) + except ValueError, ev: + if options.format == 'six': + stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) ) + else: + stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) ) +# strout += str(startLoc) + '\n' +# strout += str(bases) + '\n' +# strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov) + if loc == lastLoc+1 or lastLoc == -1: + if cov >= coverage: + if seq == lastSeq or lastSeq == '': + if startLoc == -1: + startLoc = loc + locs.append(loc) + bases.append(base) + else: + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + startLoc = loc + locs = [loc] + bases = [base] + else: + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + startLoc = -1 + locs = [] + bases = [] + else: + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + if cov >= coverage: + startLoc = loc + locs = [loc] + bases = [base] + else: + startLoc = -1 + locs = [] + bases = [] + lastSeq = seq + lastLoc = loc + inLine = fin.readline() + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + fout.close() + fin.close() + +# import sys +# strout += file(fout.name,'r').read() +# sys.stderr.write(strout) + +if __name__ == "__main__" : __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/pileup_interval.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,193 @@ +<tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.1"> + <description>condenses pileup format into ranges of bases</description> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <command interpreter="python"> + pileup_interval.py + --input=$input + --output=$output + --coverage=$coverage + --format=$format_type.format + #if $format_type.format == "ten": + --base=$format_type.which_base + --seq_column="None" + --loc_column="None" + --base_column="None" + --cvrg_column="None" + #elif $format_type.format == "manual": + --base="None" + --seq_column=$format_type.seq_column + --loc_column=$format_type.loc_column + --base_column=$format_type.base_column + --cvrg_column=$format_type.cvrg_column + #else: + --base="None" + --seq_column="None" + --loc_column="None" + --base_column="None" + --cvrg_column="None" + #end if + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Choose a pileup file to condense:" /> + <conditional name="format_type"> + <param name="format" type="select" label="which contains:" help="See "Types of pileup datasets" below for examples"> + <option value="six" selected="true">Pileup with six columns (simple)</option> + <option value="ten">Pileup with ten columns (with consensus)</option> + <option value="manual">Set columns manually</option> + </param> + <when value="six" /> + <when value="ten"> + <param name="which_base" type="select" label="Which base do you want to concatenate"> + <option value="first" selected="true">Reference base (first)</option> + <option value="second">Consensus base (second)</option> + </param> + </when> + <when value="manual"> + <param name="seq_column" label="Select column with sequence name" type="data_column" numerical="false" data_ref="input" /> + <param name="loc_column" label="Select column with base location" type="data_column" numerical="false" data_ref="input" /> + <param name="base_column" label="Select column with base to concatenate" type="data_column" numerical="false" data_ref="input" /> + <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" /> + </when> + </conditional> + <param name="coverage" type="integer" value="3" label="Do not report bases with coverage less than:" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <test> + <param name="input" value="pileup_interval_in1.tabular" /> + <param name="format" value="six" /> + <param name="coverage" value="3" /> + <output name="output" file="pileup_interval_out1.tabular" /> + </test> + <test> + <param name="input" value="pileup_interval_in2.tabular" /> + <param name="format" value="ten" /> + <param name="which_base" value="first" /> + <param name="coverage" value="3" /> + <output name="output" file="pileup_interval_out2.tabular" /> + </test> + <test> + <param name="input" value="pileup_interval_in2.tabular" /> + <param name="format" value="manual" /> + <param name="seq_column" value="1" /> + <param name="loc_column" value="2" /> + <param name="base_column" value="3" /> + <param name="cvrg_column" value="8" /> + <param name="coverage" value="3" /> + <output name="output" file="pileup_interval_out2.tabular" /> + </test> + </tests> + <help> + +**What is does** + +Reduces the size of a results set by taking a pileup file and producing a condensed version showing consecutive sequences of bases meeting coverage criteria. The tool works on six and ten column pileup formats produced with *samtools pileup* command. You also can specify columns for the input file manually. The tool assumes that the pileup dataset was produced by *samtools pileup* command (although you can override this by setting column assignments manually). + +-------- + +**Types of pileup datasets** + +The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. + +.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml + +**Six column pileup**:: + + 1 2 3 4 5 6 + --------------------------------- + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + +where:: + + Column Definition + ------ ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Coverage (# reads aligning over that position) + 5 Bases within reads where (see Galaxy wiki for more info) + 6 Quality values (phred33 scale, see Galaxy wiki for more) + +**Ten column pileup** + +The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: + + + 1 2 3 4 5 6 7 8 9 10 + ------------------------------------------------ + chrM 412 A A 75 0 25 2 ., II + chrM 413 G G 72 0 25 4 ..t, IIIH + chrM 414 C C 75 0 25 4 ...a III2 + chrM 415 C T 75 75 25 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Consensus bases + 5 Consensus quality + 6 SNP quality + 7 Maximum mapping quality + 8 Coverage (# reads aligning over that position) + 9 Bases within reads where (see Galaxy wiki for more info) + 10 Quality values (phred33 scale, see Galaxy wiki for more) + + +.. __: http://samtools.sourceforge.net/cns0.shtml + +------ + +**The output format** + +The output file condenses the information in the pileup file so that consecutive bases are listed together as sequences. The starting and ending points of the sequence range are listed, with the starting value converted to a 0-based value. + +Given the following input with minimum coverage set to 3:: + + 1 2 3 4 5 6 + --------------------------------- + chr1 112 G 3 ..Ta III6 + chr1 113 T 2 aT.. III5 + chr1 114 A 5 ,,.. IIH2 + chr1 115 C 4 ,., III + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + chrM 490 T 3 a I + +the following would be the output:: + + 1 2 3 4 + ------------------- + chr1 111 112 G + chr1 113 115 AC + chrM 412 415 GCC + chrM 489 490 T + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Starting position (0-based) + 3 Ending position (1-based) + 4 Sequence of bases + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + </citations> + +</tool> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/test-data/pileup_interval_in1.tabular Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,118 @@ +chr1 1 G 3 , 3 +chr1 5 A 5 , I +chr1 10 T 2 , I +chr1 11 C 3 , I +chr1 12 G 4 , I +chr1 13 C 2 , I +chr1 14 A 3 , I +chr1 15 T 3 , 6 +chr1 16 A 2 , 3 +chr1 17 T 4 , I +chr1 2735 C 3 , I +chrM 2736 t 3 , 9 +chrM 2737 t 3 , I +chrM 2738 a 3 , I +chrM 2739 c 3 , I +chrM 2740 a 3 , I +chrM 2741 c 3 , I +chrM 2742 t 4 , 5 +chrM 2743 c 5 , I +chrM 2744 a 2 , I +chrM 2745 g 1 , I +chrM 2746 a 1 , I +chrM 2747 g 1 , I +chrM 2748 g 1 , I +chrM 2749 t 1 , I +chrM 2750 t 1 , I +chrM 2751 c 1 , I +chrM 2752 a 1 , I +chrM 2753 a 1 , I +chrM 2754 c 1 , I +chrM 2755 t 1 , I +chrM 2756 c 1 , I +chrM 2757 c 1 , I +chrM 2758 t 5 , I +chrM 2759 c 3 , I +chrM 2760 t 1 , I +chrM 2761 c 1 , I +chrM 2762 c 1 n " +chrM 2763 c 1 n " +chrM 2764 t 1 , I +chrM 2765 a 1 , I +chrM 2766 a 1 , I +chrM 2767 c 1 , I +chrM 2768 a 1 , I +chrM 2769 a 1 , I +chrM 2770 c 1 ,$ I +chrM 9563 C 1 ^:, I +chrM 9564 T 1 , + +chrM 9565 G 1 , - +chrM 9566 A 1 , I +chrM 9567 C 1 , I +chrM 9568 T 1 , ? +chrM 9569 A 1 , I +chrM 9570 C 1 , D +chrM 9571 C 1 , I +chrM 9572 A 1 , I +chrM 9573 C 1 , I +chrM 9574 A 1 , I +chrM 9575 A 1 , I +chrM 9576 C 1 , I +chrM 9577 T 1 , I +chrM 9578 A 1 , I +chrM 9579 A 1 , I +chrM 9580 A 1 , I +chrM 9581 C 1 , I +chrM 9582 A 1 , I +chrM 9583 T 1 , I +chrM 9584 C 1 , I +chrM 9585 T 1 , I +chrM 9586 A 1 , I +chrM 9587 T 1 , I +chrM 9588 G 1 , I +chrM 9589 C 1 , I +chrM 9590 A 1 n " +chrM 9591 G 1 n " +chrM 9592 A 1 , I +chrM 9593 A 1 , I +chrM 9594 A 1 , I +chrM 9595 A 1 , I +chrM 9596 A 1 , I +chrM 9597 A 1 , I +chrM 9598 C 1 ,$ I +chrM 10864 T 1 ^!, ~ +chrM 10865 G 1 , ~ +chrM 10866 T 1 , ~ +chrM 10867 A 1 , ~ +chrM 10868 G 1 , ~ +chrM 10869 A 1 , ~ +chrM 10870 A 1 , ~ +chrM 10871 G 1 , ~ +chrM 10872 C 1 , ~ +chrM 10873 C 3 , ~ +chrM 10874 C 3 , ~ +chrM 10875 C 3 , ~ +chrM 10876 A 3 , ~ +chrM 10877 A 3 , ~ +chrM 10878 T 3 , ~ +chrM 10879 T 3 , ~ +chrM 10880 G 3 , ~ +chrM 10881 C 3 , ~ +chrM 10882 C 3 , ~ +chrM 10883 G 3 , ~ +chrM 10884 G 3 , ~ +chrM 10885 A 1 , ~ +chrM 10886 T 1 , ~ +chrM 10887 C 1 , ~ +chrM 10888 C 1 , ~ +chrM 10889 A 1 , ~ +chrM 10890 T 1 , ~ +chrM 10891 A 1 n ~ +chrM 10892 G 1 n ~ +chrM 10893 T 1 , ~ +chrM 10894 G 1 , ~ +chrM 10895 C 1 , ~ +chrM 10896 T 3 , ~ +chrM 10897 A 3 , ~ +chrM 10898 G 3 , ~ +chrM 10899 C 3 ,$ ~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/test-data/pileup_interval_in2.tabular Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,99 @@ +chr1 5016020 t T 33 0 25 2 .. II +chr1 5016021 g G 32 0 25 2 .. )I +chr1 5016022 t T 28 0 25 2 .. I$ +chr1 5016023 t T 33 0 25 2 .. II +chr1 5016024 t T 33 0 25 2 .. II +chr1 5016025 c C 39 0 25 4 ..^:,^:, II:/ +chr1 5016026 t T 28 0 25 4 ..,c III$ +chr1 5016027 c C 39 0 25 4 ..,, H0+7 +chr1 5016028 t T 28 0 25 4 ..,g III$ +chr1 5016029 g G 10 0 25 4 T.,t BII# +chr1 5016030 c C 39 0 25 4 .$.$,, @)6I +chr1 5016031 t T 33 0 25 2 ,, IF +chr1 5016032 t G 0 0 25 2 ,g IC +chr1 5016033 c C 33 0 25 2 ,, 1I +chr1 5016034 t T 33 0 25 2 ,, II +chr1 12459316 G G 7 0 0 2 .. II +chr1 12459317 G G 7 0 0 2 .. II +chr1 12459318 A A 10 0 0 3 ..^!. III +chr1 12459319 T T 10 0 0 3 ... III +chr1 12459320 C C 10 0 0 3 ... III +chr1 12459321 T T 10 0 0 3 ... III +chr1 12459322 A A 10 0 0 3 ... .II +chr1 12459323 C C 10 0 0 3 ... ?II +chr1 12459324 A A 10 0 0 3 ... G?I +chr1 12459325 C C 10 0 0 3 ... II; +chr1 12459326 A A 10 0 0 3 ... I@B +chr1 12459327 C C 10 0 0 3 ... 8II +chr1 12459328 A A 10 0 0 3 ... IH5 +chr1 12459329 T T 10 0 0 3 ... I;I +chr1 12459330 C C 10 0 0 3 ... IAI +chr1 12459331 T T 10 0 0 3 ... 3HI +chr1 49116109 C C 28 0 18 2 .. G? +chr1 49116110 A A 28 0 18 2 .. '@ +chr1 49116111 G G 26 0 18 2 .. 68 +chr1 49116112 A A 9 0 18 2 .. 1' +chr1 49116113 G G 20 0 18 2 .. I2 +chr1 49116114 G G 2 0 20 3 A.^:, &&$ +chr1 49116115 G G 21 0 20 3 .A, 8$I +chr1 49116116 T T 31 0 20 3 .., .9% +chr1 49116117 T T 36 0 20 3 .., I55 +chr1 49116118 T T 36 0 20 3 .., II+ +chr1 49116119 T T 36 0 20 3 .., II8 +chr1 49116120 G G 32 0 20 3 .., &%B +chr1 49116121 T T 36 0 20 3 .$., <63 +chr1 49116122 C C 33 0 25 2 ., +I +chr1 49116123 T T 33 0 25 2 ., -7 +chr1 49116124 G G 29 0 25 2 ., %I +chr1 49116125 C C 24 0 25 2 .$, +/ +chr1 126866554 G G 7 0 0 2 .. (I +chr1 126866555 C C 10 0 0 3 .$.^!. III +chr1 126866556 C C 7 0 0 2 .. II +chr11 1021425 C C 4 0 0 1 . I +chr11 1021426 A A 4 0 0 1 . I +chr11 1021427 G G 4 0 0 1 . I +chr11 1021428 G G 28 0 18 2 .^:. 0I +chr11 1021429 G G 19 0 18 2 C. $I +chr11 1021430 G G 36 0 20 3 ..^:. III +chr11 1021431 T T 36 0 20 3 ... III +chr11 1021432 G G 36 0 20 3 ... III +chr11 1021433 A A 36 0 20 3 ... @II +chr11 1021434 C C 36 0 20 3 ... %II +chr11 1021435 G G 36 0 20 3 ... #II +chr11 1021436 T T 36 0 20 3 ... 8II +chr11 1021437 G G 36 0 20 3 ... /II +chr11 1021438 G G 36 0 20 3 ... III +chr11 1021439 G G 36 0 20 3 ... ;II +chr11 1021440 C C 28 0 20 3 N.. "II +chr11 1021441 T T 36 0 20 3 ... IFI +chr11 1021442 G G 36 0 20 3 ... III +chr11 1021443 T T 36 0 20 3 ... III +chr11 1021444 G G 28 0 20 3 T.. #II +chr11 1021445 T T 28 0 20 3 C.. #II +chr11 1021446 C C 36 0 20 3 .$.. :II +chr11 1021447 T T 33 0 25 2 .. II +chr11 1021448 G G 33 0 25 2 .. II +chr11 1021449 T T 33 0 25 2 .. 7I +chr11 1021450 G G 33 0 25 2 .. II +chr14 1021451 T A 33 0 25 3 .. 4I +chr14 80839355 A A 33 0 25 2 .. I* +chr14 80839356 G G 28 0 25 2 .. I# +chr14 80839357 A A 31 0 25 2 .. I( +chr14 80839358 A A 32 0 25 2 .. I) +chr14 80839359 T T 39 0 25 4 ..^:,^:, I+I( +chr14 80839360 T T 39 0 25 4 ..,, I+I+ +chr14 80839361 C C 39 0 25 4 ..,, I&5( +chr14 80839362 T T 39 0 25 4 ..,, I3II +chr14 80839363 G G 39 0 25 4 ..,, G#I4 +chr14 80839364 G G 39 0 25 4 ..,, I'II +chr14 80839365 A A 39 0 25 4 ..,, @)IH +chr14 80839366 T T 39 0 25 4 ..,, I/I2 +chr14 80839367 A A 39 0 25 4 ..,, I,I= +chr14 80839368 T T 39 0 25 4 ..,, I.I7 +chr14 80839369 T T 39 0 25 4 ..,, I4II +chr14 80839370 T T 39 0 25 4 ..,, I2I0 +chr14 80839371 A A 39 0 25 4 .$.$,, ;+I? +chr14 80839372 C C 14 0 25 2 ,a 5$ +chr14 80839373 A A 33 0 25 2 ,, II +chr14 80839374 T T 33 0 25 2 ,, II +chr14 80839375 T T 33 0 25 2 ,, I?
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/test-data/pileup_interval_out1.tabular Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,10 @@ +chr1 0 1 G +chr1 4 5 A +chr1 10 12 CG +chr1 13 15 AT +chr1 16 17 T +chr1 2734 2735 C +chrM 2735 2743 ttacactc +chrM 2757 2759 tc +chrM 10872 10884 CCCAATTGCCGG +chrM 10895 10899 TAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/test-data/pileup_interval_out2.tabular Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,7 @@ +chr1 5016024 5016030 ctctgc +chr1 12459317 12459331 ATCTACACACATCT +chr1 49116113 49116121 GGTTTTGT +chr1 126866554 126866555 C +chr11 1021429 1021446 GTGACGTGGGCTGTGTC +chr14 1021450 1021451 T +chr14 80839358 80839371 TTCTGGATATTTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/pileup_interval/0b4181be05c8/pileup_interval/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/sam_to_bam.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,84 @@ +<tool id="sam_to_bam" name="SAM-to-BAM" version="2.0"> + <description>convert SAM to BAM</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="version_command"></expand> + <expand macro="stdio"></expand> + <command> + <![CDATA[ + samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && + #if $source.index_source == "history": + ln -s $source.ref_file input.fa && + samtools faidx input.fa && + #else + ln -s ${source.index.fields.path} input.fa && + ln -s ${source.index.fields.path}.fai input.fa.fai && + #end if + samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam + ]]> + </command> + <inputs> + <conditional name="source"> + <param label="Choose the source for the reference genome" name="index_source" type="select"> + <option value="cached">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="cached"> + <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> + </param> + <param label="Using reference genome" name="index" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="1" key="dbkey" ref="input1" type="data_meta" /> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param format="sam" label="SAM file to convert" name="input1" type="data" /> + <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1"> + <actions> + <conditional name="source.index_source"> + <when value="cached"> + <action name="dbkey" type="metadata"> + <option name="source.input1" param_attribute="dbkey" type="from_param" /> + </action> + </when> + <when value="history"> + <action name="dbkey" type="metadata"> + <option name="source.ref_file" param_attribute="dbkey" type="from_param" /> + </action> + </when> + </conditional> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="index_source" value="history" /> + <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" /> + <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> + <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands:: + + samtools sort -O bam -o sorted_input.bam [INPUT SAM] + samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam + +]]> + </help> + <expand macro="citations"></expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/cached_locally/all_fasta.loc Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1 @@ +chrM chr_m Horse (Equus caballus): equCab2 chrM ${__HERE__}/chrM.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/cached_locally/chr_m.fasta Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,335 @@ +>chrM +GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA +GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT +TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT +CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA +AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG +ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG +GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA +ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA +AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA +AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA +TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA +AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT +GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC +CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT +CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA +AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT +TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC +TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT +GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT +CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA +CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG +TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA +TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC +TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG +AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG +ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT +AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC +CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT +ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG +AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA +ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA +AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA +ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG +TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA +ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG +TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA +CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA +TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA +AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT +ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC +AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca +taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt +tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg +cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG +ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT +TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC +CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA +TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG +CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG +TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT +CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT +CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT +AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA +AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg +tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt +caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT +GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT +CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG +GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA +CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT +AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC +CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC +CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA +CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG +TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC +ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC +ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA +ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA +TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA +ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG +GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC +ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA +CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC +TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA +CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT +ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact +acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa +ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT +ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT +CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA +TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA +GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC +CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA +TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA +GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA +ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA +TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA +ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT +AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC +AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA +TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT +ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA +GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT +CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC +CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA +AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC +AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT +CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA +TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA +ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC +CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC +TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT +TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT +TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC +CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC +TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG +AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG +CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA +GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG +AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC +TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC +GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA +CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA +TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC +GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC +TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA +TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC +TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA +AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC +TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT +AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT +TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA +TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT +AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT +TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA +TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT +ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG +AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT +TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA +GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT +CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT +TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC +TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT +CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT +ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA +GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG +AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG +GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA +AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata +tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC +ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG +GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA +AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA +GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC +CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT +ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT +ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC +CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT +TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC +TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA +ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT +AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG +TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA +TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA +CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA +TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT +GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT +AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT +ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC +CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA +ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT +CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC +AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC +AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT +TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA +CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA +GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT +ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA +CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT +AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT +AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC +TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC +GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC +CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC +AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC +ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT +ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG +CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT +TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC +CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC +AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG +TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA +GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT +AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT +TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG +TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT +CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG +AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG +TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA +CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA +AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT +ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA +GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC +TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA +AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA +ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC +CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA +TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT +TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC +ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC +ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA +TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC +TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT +CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC +TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT +GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA +TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG +CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC +TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC +CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT +AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA +TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC +ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT +CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT +CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA +AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG +TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC +TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA +GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT +ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC +TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA +AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT +AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA +TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA +AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA +AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA +ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA +ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA +TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC +GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA +GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT +TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA +AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC +CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA +TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA +CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC +CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT +CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA +TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC +TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC +CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG +TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA +TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC +ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC +TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA +TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT +TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC +TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC +AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA +ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC +CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC +GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT +CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA +TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC +TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA +CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT +TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC +CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT +AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT +ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC +TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG +TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC +TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC +CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA +CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG +CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG +ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC +CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG +CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC +TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC +CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT +CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG +TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA +ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC +CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA +CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT +AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC +AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG +TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC +ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC +CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG +AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA +ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT +GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC +GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA +CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG +AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT +ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA +GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC +AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG +GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC +ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT +ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT +ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC +AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT +CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT +CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC +CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT +CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA +ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA +TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT +AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC +CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC +CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT +CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT +CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC +ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT +ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC +TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC +TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT +CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC +CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG +TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA +GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC +AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC +GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG +CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT +TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA +ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA +CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT +CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA +CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA +GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac +ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct +gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt +gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc +acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac +ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA +CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT +GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT +AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA +GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT +TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC +TTCTTCCCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/cached_locally/chr_m.fasta.fai Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1 @@ +chrM 16660 6 50 51
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/cached_locally/fasta_indexes.loc Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1 @@ +chrM chr_m Horse (Equus caballus): equCab2 chrM ${__HERE__}/chrM.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/chr_m.fasta Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,335 @@ +>chrM +GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA +GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT +TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT +CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA +AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG +ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG +GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA +ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA +AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA +AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA +TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA +AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT +GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC +CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT +CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA +AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT +TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC +TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT +GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT +CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA +CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG +TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA +TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC +TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG +AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG +ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT +AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC +CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT +ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG +AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA +ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA +AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA +ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG +TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA +ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG +TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA +CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA +TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA +AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT +ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC +AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca +taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt +tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg +cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG +ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT +TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC +CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA +TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG +CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG +TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT +CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT +CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT +AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA +AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg +tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt +caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT +GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT +CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG +GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA +CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT +AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC +CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC +CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA +CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG +TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC +ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC +ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA +ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA +TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA +ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG +GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC +ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA +CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC +TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA +CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT +ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact +acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa +ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT +ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT +CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA +TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA +GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC +CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA +TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA +GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA +ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA +TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA +ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT +AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC +AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA +TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT +ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA +GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT +CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC +CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA +AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC +AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT +CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA +TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA +ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC +CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC +TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT +TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT +TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC +CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC +TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG +AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG +CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA +GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG +AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC +TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC +GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA +CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA +TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC +GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC +TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA +TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC +TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA +AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC +TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT +AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT +TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA +TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT +AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT +TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA +TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT +ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG +AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT +TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA +GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT +CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT +TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC +TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT +CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT +ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA +GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG +AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG +GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA +AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata +tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC +ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG +GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA +AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA +GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC +CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT +ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT +ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC +CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT +TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC +TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA +ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT +AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG +TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA +TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA +CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA +TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT +GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT +AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT +ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC +CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA +ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT +CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC +AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC +AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT +TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA +CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA +GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT +ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA +CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT +AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT +AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC +TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC +GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC +CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC +AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC +ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT +ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG +CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT +TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC +CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC +AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG +TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA +GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT +AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT +TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG +TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT +CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG +AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG +TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA +CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA +AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT +ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA +GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC +TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA +AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA +ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC +CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA +TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT +TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC +ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC +ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA +TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC +TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT +CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC +TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT +GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA +TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG +CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC +TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC +CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT +AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA +TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC +ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT +CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT +CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA +AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG +TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC +TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA +GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT +ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC +TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA +AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT +AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA +TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA +AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA +AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA +ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA +ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA +TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC +GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA +GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT +TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA +AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC +CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA +TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA +CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC +CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT +CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA +TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC +TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC +CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG +TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA +TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC +ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC +TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA +TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT +TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC +TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC +AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA +ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC +CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC +GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT +CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA +TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC +TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA +CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT +TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC +CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT +AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT +ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC +TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG +TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC +TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC +CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA +CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG +CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG +ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC +CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG +CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC +TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC +CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT +CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG +TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA +ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC +CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA +CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT +AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC +AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG +TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC +ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC +CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG +AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA +ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT +GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC +GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA +CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG +AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT +ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA +GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC +AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG +GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC +ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT +ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT +ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC +AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT +CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT +CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC +CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT +CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA +ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA +TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT +AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC +CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC +CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT +CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT +CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC +ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT +ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC +TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC +TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT +CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC +CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG +TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA +GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC +AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC +GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG +CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT +TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA +ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA +CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT +CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA +CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA +GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac +ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct +gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt +gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc +acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac +ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA +CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT +GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT +AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA +GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT +TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC +TTCTTCCCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/chr_m.fasta.fai Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1 @@ +chrM 16660 6 50 51
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/test-data/sam_to_bam_in1.sam Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,13 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chrM LN:100001 +@RG ID:rg1 SM:s1 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/tool-data/fasta_indexes.loc.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/tool_data_table_conf.xml.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/tool_data_table_conf.xml.test Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,10 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/fasta_indexes.loc" /> + </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" /> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/sam_to_bam/d04d9f1c6791/sam_to_bam/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/samtools_bedcov.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,57 @@ +<tool id="samtools_bedcov" name="BedCov" version="2.0"> + <description>calculate read depth for a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[ + for bamfile in + #for dataset in $input_bams: + "${dataset}" + #end for + ; do + if [ ! -f \$bamfile.bai ] ; then + ln -s \$bamfile && samtools index `basename \$bamfile` ; + else + ln -s \$bamfile && ln -s \$bamfile.bai ; + fi ; + done ; + samtools bedcov "${input_bed}" + #for dataset in $input_bams: + `basename "${dataset}"` + #end for + > "${output}" + ]]> + </command> + <inputs> + <param name="input_bed" type="data" format="bed" label="BED file" /> + <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <output name="output" file="samtools_bedcov_out1.tab" /> + </test> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> + <output name="output" file="samtools_bedcov_out2.tab" /> + </test> + </tests> + <help> +**What it does** + +Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command:: + + samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT] + + </help> + <expand macro="citations"></expand> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/test-data/eboVir3.1.bed Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 +eboVir3 1500 2000 +eboVir3 1500 3000
Binary file samtools/samtools_bedcov/8c3472790020/samtools_bedcov/test-data/eboVir3.2.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/test-data/eboVir3.2.bed Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 +eboVir3 1500 2000 +eboVir3 1500 3000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/test-data/samtools_bedcov_out1.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 +eboVir3 1500 2000 3009 +eboVir3 1500 3000 9986
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/test-data/samtools_bedcov_out2.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 2094 +eboVir3 1500 2000 3009 1064 +eboVir3 1500 3000 9986 3455
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_bedcov/8c3472790020/samtools_bedcov/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/samtools_calmd.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,99 @@ +<tool id="samtools_calmd" name="CalMD" version="2.0"> + <description>recalculate MD/NM tags</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[ + #if str( $reference_source.reference_source_selector ) == "history": + #set ref_fa = 'ref.fa' + ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && + #else: + #set ref_fa = str( $reference_source.ref_fasta.fields.path ) + #end if + samtools calmd + #if str($option_set.option_sets) == 'advanced': + $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq + #end if + -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> + </command> + <inputs> + <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="cached"> + <param name="ref_fasta" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" column="0" key="dbkey" ref="input_bam" /> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <conditional name="option_set"> + <param name="option_sets" type="select" label="Options"> + <option value="default">Use defaults</option> + <option value="advanced">Advanced options</option> + </param> + <when value="default" /> + <when value="advanced"> + <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/> + <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/> + <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/> + <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="option_sets" value="default" /> + <param name="input_bam" value="phiX.bam"/> + <param name="reference_source_selector" value="history" /> + <param name="ref_fasta" value="phiX.fasta" /> + <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> + </test> + <test> + <param name="option_sets" value="advanced" /> + <param name="change_identical" value="true" /> + <param name="extended_baq" value="true" /> + <param name="input_bam" value="phiX.bam"/> + <param name="reference_source_selector" value="history" /> + <param name="ref_fasta" value="phiX.fasta" /> + <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> + </test> + </tests> + <help> +**What it does** + +Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options:: + + -e change identical bases to '=' + -A modify the quality string + -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A) + -E extended BAQ for better sensitivity but lower specificity + +----- + +**NM and MD tags** + +From SAM format specification:: + + MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 + NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping + +See refernces for more information about SAM format tags. + + </help> + <expand macro="citations"></expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/test-data/phiX.fasta Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
Binary file samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/test-data/samtools_calmd_out_1.bam has changed
Binary file samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/test-data/samtools_calmd_out_2.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/tool-data/fasta_indexes.loc.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/tool_data_table_conf.xml.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,7 @@ +<?xml version="1.0" encoding="utf-8"?> +<tables> + <table comment_char="#" name="fasta_indexes"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_calmd/1ebb4ecdc1ef/samtools_calmd/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_flagstat/0072bf593791/samtools_flagstat/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_flagstat/0072bf593791/samtools_flagstat/samtools_flagstat.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,45 @@ +<tool id="samtools_flagstat" name="Flagstat" version="2.0"> + <description>tabulate descriptive stats for BAM datset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command>samtools flagstat "$input1" > "$output1" + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File to Convert" /> + </inputs> + <outputs> + <data name="output1" format="txt" /> + </outputs> + <tests> + <test> + <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> + <output name="output1" file="samtools_flagstat_out1.txt" /> + </test> + </tests> + <help> + +**What it does** + +Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: + + 200 + 0 in total (QC-passed reads + QC-failed reads) + 0 + 0 secondary + 0 + 0 supplementary + 0 + 0 duplicates + 25 + 0 mapped (12.50%:nan%) + 200 + 0 paired in sequencing + 100 + 0 read1 + 100 + 0 read2 + 0 + 0 properly paired (0.00%:nan%) + 0 + 0 with itself and mate mapped + 25 + 0 singletons (12.50%:nan%) + 0 + 0 with mate mapped to a different chr + 0 + 0 with mate mapped to a different chr (mapQ>=5) + + </help> + <expand macro="citations"></expand> +</tool>
Binary file samtools/samtools_flagstat/0072bf593791/samtools_flagstat/test-data/samtools_flagstat_input1.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_flagstat/0072bf593791/samtools_flagstat/test-data/samtools_flagstat_out1.txt Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,13 @@ +200 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 secondary +0 + 0 supplementary +0 + 0 duplicates +25 + 0 mapped (12.50%:nan%) +200 + 0 paired in sequencing +100 + 0 read1 +100 + 0 read2 +0 + 0 properly paired (0.00%:nan%) +0 + 0 with itself and mate mapped +25 + 0 singletons (12.50%:nan%) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_flagstat/0072bf593791/samtools_flagstat/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_idxstats/87398ae795c7/samtools_idxstats/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_idxstats/87398ae795c7/samtools_idxstats/samtools_idxstats.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,72 @@ +<tool id="samtools_idxstats" name="IdxStats" version="2.0"> + <description>tabulate mapping statistics for BAM dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[ +if [ ! -f "${input}.bai" ] ; then + ln -s "${input}" input.bam ; + samtools sort -o sorted.bam -O bam -T sts "${input}" ; + samtools index sorted.bam ; + samtools idxstats sorted.bam > "${output}" ; +else + samtools idxstats "${input}" > "${output}" ; +fi]]> + </command> + <inputs> + <param name="input" type="data" format="bam" label="BAM file" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="phiX.bam" ftype="bam" /> + <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file. + +Input is a sorted and indexed BAM file, the output is tabular with +four columns (one row per reference sequence plus a final line for +unmapped reads):: + + Column Description + ------ ----------------------------- + 1 Reference sequence identifier + 2 Reference sequence length + 3 Number of mapped reads + 4 Number of placed but unmapped reads + (typically unmapped partners of mapped reads) + +------ + +**Example** output from a *de novo* assembly:: + + contig_1 170035 98397 0 + contig_2 403835 199564 0 + contig_3 553102 288189 0 + ... ... ... ... + contig_603 653 50 0 + contig_604 214 6 0 + \* 0 0 50320 + + +In this example there were 604 contigs, each with one line in the output table, +plus the final row (labelled with an asterisk) representing 50320 unmapped reads. +In this BAM file, the final column was otherwise zero. + +------ + +Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command +]]> + </help> + <expand macro="citations"></expand> +</tool>
Binary file samtools/samtools_idxstats/87398ae795c7/samtools_idxstats/test-data/phiX.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_idxstats/87398ae795c7/samtools_idxstats/test-data/samtools_idxstats_out.tabular Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,2 @@ +phiX174 5386 972 18 +* 0 0 10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_idxstats/87398ae795c7/samtools_idxstats/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/samtools_mpileup.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,372 @@ +<tool id="samtools_mpileup" name="MPileup" version="2.0"> + <description>call variants</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + <![CDATA[ + #if $reference_source.reference_source_selector == "history": + ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup + #else: + samtools mpileup + #end if + #if $reference_source.reference_source_selector != "history": + -f "${reference_source.ref_file.fields.path}" + #else: + -f "${reference_source.ref_file}" + #end if + #for $i, $input_bam in enumerate( $reference_source.input_bams ): + "${input_bam.input_bam}" + #end for + #if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter": + #if $advanced_options.filter_by_flags.require_flags: + --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])} + #end if + #if $advanced_options.filter_by_flags.exclude_flags: + --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])} + #end if + #end if + #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": + -l "$pasted_regions" + #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history" + -l "$advanced_options.limit_by_region.bed_regions" + #end if + #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": + -G "$excluded_read_groups" + #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history" + -G "$advanced_options.exclude_read_group.read_groups" + #end if + ${advanced_options.skip_anomalous_read_pairs} + ${advanced_options.disable_probabilistic_realignment} + -C "${advanced_options.coefficient_for_downgrading}" + -d "${advanced_options.max_reads_per_bam}" + ${advanced_options.extended_BAQ_computation} + -q "${advanced_options.minimum_mapping_quality}" + -Q "${advanced_options.minimum_base_quality}" + #if str( $advanced_options.region_string ): + -r "${advanced_options.region_string}" + #end if + + #end if + #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation': + ## + + ${genotype_likelihood_computation_type.output_format} + ${genotype_likelihood_computation_type.compressed} + + #if str( $genotype_likelihood_computation_type.output_tags ) != "None": + -output-tags "${genotype_likelihood_computation_type.output_tags}" + #end if + + #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling': + -o "${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}" + -e "${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}" + -h "${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" + -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}" + -m "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" + --open-prob "${genotype_likelihood_computation_type.perform_indel_calling.open_seq_error_probability}" + -F "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}" + ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample} + #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ): + -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }" + #end if + #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling': + -I + #end if + + + #else: + ${genotype_likelihood_computation_type.base_position_on_reads} + ${genotype_likelihood_computation_type.output_mapping_quality} + #end if + --output "$output_mpileup" 2> "$output_log" + ]]> + </command> + <inputs> + <conditional name="reference_source"> + <param label="Choose the source for the reference genome" name="reference_source_selector" type="select"> + <option value="cached">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="cached"> + <repeat min="1" name="input_bams" title="BAM file"> + <param format="bam" label="BAM file" name="input_bam" type="data"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> + </param> + </repeat> + <param label="Using reference genome" name="ref_file" type="select"> + <options from_data_table="fasta_indexes" /> + </param> + </when> + <when value="history"> + <repeat min="1" name="input_bams" title="BAM file"> + <param format="bam" label="BAM file" name="input_bam" type="data"> + <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> + </param> + </repeat> + <param format="fasta" label="Using reference genome" name="ref_file" type="data" /> + </when> + </conditional> + <conditional name="genotype_likelihood_computation_type"> + <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select"> + <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option> + <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option> + </param> + <when value="perform_genotype_likelihood_computation"> + <param label="Choose the output format" name="output_format" type="select"> + <option value="--VCF">VCF</option> + <option value="--BCF">BCF</option> + </param> + <param checked="False" falsevalue="--uncompressed" label="Compress output" name="compressed" truevalue="" type="boolean" help="--incompressed; default=False"/> + <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags"> + <option value="DP">DP (Number of high-quality bases)</option> + <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option> + <option value="DV">DV (Number of high-quality non-reference bases)</option> + <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option> + <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option> + <option value="SP">SP (Phred-scaled strand bias P-value)</option> + </param> + <conditional name="perform_indel_calling"> + <param label="Perform INDEL calling" name="perform_indel_calling_selector" type="select"> + <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option> + <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option> + <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> + </param> + <when value="perform_indel_calling_def" /> + <when value="perform_indel_calling"> + <param label="Phred-scaled gap open sequencing error probability" name="gap_open_sequencing_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> + <param label="Phred-scaled gap extension sequencing error probability" name="gap_extension_sequencing_error_probability" type="integer" value="20" help="--ext-prob; Reducing this value leads to longer indels. default=20"/> + <param label="Coefficient for modeling homopolymer errors." name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" help="--tandem-qual; default=100"/> + <param label="Skip INDEL calling if the average per-sample depth is above" name="skip_indel_calling_above_sample_depth" type="integer" value="250" help="--max-idepth; default=250"/> + <param label="Minimum gapped reads for indel candidates" name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" help="--min-ireads; default=1"/> + <param label="Phred-scaled gap open sequencing error probability" name="open_seq_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> + <param label="Minimum fraction of gapped reads" name="minimum_gapped_read_fraction" type="float" value="0.002" help="--gap-frac; default=0.002"/> + <param checked="False" falsevalue="" label="Apply --min-ireads and --gap-frac values on a per-sample basis" name="gapped_read_per_sample" truevalue="-p" type="boolean" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/> + <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> + <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/> + </repeat> + </when> + <when value="do_not_perform_indel_calling" /> + </conditional> + + </when> + <when value="do_not_perform_genotype_likelihood_computation"> + <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/> + <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/> + </when> + </conditional> + <conditional name="advanced_options"> + <param label="Set advanced options" name="advanced_options_selector" type="select"> + <option selected="True" value="basic">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="advanced"> + <conditional name="filter_by_flags"> + <param label="Set filter by flags" name="filter_flags" type="select"> + <option selected="True" value="nofilter">Do not filter</option> + <option value="filter">Filter by flags to exclude or require</option> + </param> + <when value="filter"> + <param display="checkboxes" label="Require" multiple="True" name="require_flags" type="select" help="--incl-flags"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate 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">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + <param display="checkboxes" label="Exclude" multiple="True" name="exclude_flags" type="select" help="--excl-flags"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate 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">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + </when> + <when value="nofilter" /> + </conditional> + <conditional name="limit_by_region"> + <param label="Select regions to call" name="limit_by_regions" type="select"> + <option selected="True" value="no_limit">Do not limit</option> + <option value="history">From an uploaded BED file (--positions)</option> + <option value="paste">Paste a list of regions or BED (--region)</option> + </param> + <when value="history"> + <param format="bed" label="BED file" name="bed_regions" type="data" help="--positions"> + <validator type="dataset_ok_validator" /> + </param> + </when> + <when value="paste"> + <param area="true" help="Paste a list of regions in BED format or as a list of chromosomes and positions" label="Regions" name="region_paste" size="10x35" type="text"/> + </when> + <when value="no_limit" /> + </conditional> + <conditional name="exclude_read_group"> + <param label="Select read groups to exclude" name="exclude_read_groups" type="select" help="--exclude-RG"> + <option selected="True" value="no_limit">Do not exclude</option> + <option value="history">From an uploaded text file</option> + <option value="paste">Paste a list of read groups</option> + </param> + <when value="history"> + <param format="txt" label="Text file" name="read_groups" type="data"> + <validator type="dataset_ok_validator" /> + </param> + </when> + <when value="paste"> + <param area="true" help="Paste a list of read groups" label="Read groups" name="group_paste" size="10x35" type="text" /> + </when> + <when value="no_limit" /> + </conditional> + <param checked="False" falsevalue="" label="Disable read-pair overlap detection" name="ignore_overlaps" truevalue="-x" type="boolean" help="--ignore-overlaps"/> + <param checked="False" falsevalue="" label="Do not skip anomalous read pairs in variant calling" name="skip_anomalous_read_pairs" truevalue="-A" type="boolean" help="--count-orphans"/> + <param checked="False" falsevalue="" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" name="disable_probabilistic_realignment" truevalue="-B" type="boolean" help="--no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments"/> + <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/> + <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/> + <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/> + <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/> + <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/> + <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" /> + </when> + <when value="basic" /> + </conditional> + </inputs> + <outputs> + <data format="pileup" label="${tool.name} on ${on_string}" name="output_mpileup"> + <change_format> + <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" /> + <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" /> + </change_format> + </data> + <data format="txt" label="${tool.name} on ${on_string} (log)" name="output_log" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param ftype="fasta" name="ref_file" value="phiX.fasta" /> + <param ftype="bam" name="input_bam" value="samtools_mpileup_in_1.bam" /> + <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" /> + <param name="advanced_options_selector" value="basic" /> + <param name="base_position_on_reads" value="true" /> + <param name="output_mapping_quality" value="true" /> + <output file="samtools_mpileup_out_1.pileup" name="output_mpileup" /> + <output file="samtools_mpileup_out_1.log" name="output_log" /> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param ftype="fasta" name="ref_file" value="phiX.fasta" /> + <param ftype="bam" name="input_bam" value="phiX.bam" /> + <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> + <param name="gap_extension_sequencing_error_probability" value="20" /> + <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> + <param name="perform_indel_calling_selector" value="perform_indel_calling" /> + <param name="skip_indel_calling_above_sample_depth" value="250" /> + <param name="gap_open_sequencing_error_probability" value="40" /> + <param name="platform_list_repeat" value="0" /> + <param name="advanced_options_selector" value="basic" /> + <param name="genotype_likelihood_computation_type|output_format" value="VCF" /> + <output file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" name="output_mpileup" /> + <output file="samtools_mpileup_out_2.log" name="output_log" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. + +------ + +**Input options**:: + + -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding + -A, --count-orphans do not discard anomalous read pairs + -b, --bam-list FILE list of input BAM filenames, one per line + -B, --no-BAQ disable BAQ (per-Base Alignment Quality) + -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0] + -d, --max-depth INT max per-BAM depth; avoids excessive memory usage [250] + -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs + -f, --fasta-ref FILE faidx indexed reference sequence file + -G, --exclude-RG FILE exclude read groups listed in FILE + -l, --positions FILE skip unlisted positions (chr pos) or regions (BED) + -q, --min-MQ INT skip alignments with mapQ smaller than INT [0] + -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13] + -r, --region REG region in which pileup is generated + -R, --ignore-RG ignore RG tags (one BAM = one sample) + --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset [] + --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set + [UNMAP,SECONDARY,QCFAIL,DUP] + -x, --ignore-overlaps disable read-pair overlap detection + +**Output options**:: + + -o, --output FILE write output to FILE [standard output] + -g, --BCF generate genotype likelihoods in BCF format + -v, --VCF generate genotype likelihoods in VCF format + +**Output options for mpileup format** (without -g/-v):: + + -O, --output-BP output base positions on reads + -s, --output-MQ output mapping quality + +**Output options for genotype likelihoods** (when -g/-v is used):: + + -t, --output-tags LIST optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP [] + -u, --uncompressed generate uncompressed VCF/BCF output + +**SNP/INDEL genotype likelihoods options** (effective with -g/-v):: + + -e, --ext-prob INT Phred-scaled gap extension seq error probability [20] + -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002] + -h, --tandem-qual INT coefficient for homopolymer errors [100] + -I, --skip-indels do not perform indel calling + -L, --max-idepth INT maximum per-sample depth for INDEL calling [250] + -m, --min-ireads INT minimum number gapped reads for indel candidates [1] + -o, --open-prob INT Phred-scaled gap open seq error probability [40] + -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity + -P, --platforms STR comma separated list of platforms for indels [all] + +**Notes**: Assuming diploid individuals. +]]> + </help> + <configfiles> + <configfile name="excluded_read_groups"> +<![CDATA[ +#set pasted_data = '' +#if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": + #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() ) + #end if +#end if +${pasted_data} +]]> + </configfile> + <configfile name="pasted_regions"> +<![CDATA[ +#set pasted_data = '' +#if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": + #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() ) + #end if +#end if +${pasted_data} +]]> + </configfile> + </configfiles> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/phiX.fasta Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
Binary file samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/phiX_1.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools/mpileup/samtools_mpileup_out_1.log Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,2 @@ +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools/mpileup/samtools_mpileup_out_1.pileup Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,43 @@ +phiX174 1411 A 1 ^P. $ +phiX174 1412 G 3 .^D.^F. "$$ +phiX174 1413 C 5 ...^D.^F. """$$ +phiX174 1414 G 6 .....^F. #####$ +phiX174 1415 C 7 ......^F. %%%%%%& +phiX174 1416 C 8 .......^F. $$$$$$$$ +phiX174 1417 G 9 ........^F. "#######$ +phiX174 1418 T 10 .........^F. """""""""$ +phiX174 1419 G 10 .......... """""'&'%$ +phiX174 1420 G 10 .......... """""""""" +phiX174 1421 A 10 .......... """""""""" +phiX174 1422 T 10 .......... """""""""" +phiX174 1423 G 10 .......... """""""""# +phiX174 1424 C 10 ..A.AAAAAA %""""""""" +phiX174 1425 C 10 .......... $$$""""""" +phiX174 1426 T 10 .......... #####""""" +phiX174 1427 G 10 .......... ######"""" +phiX174 1428 A 10 .......... """""""""" +phiX174 1429 C 10 .......... ((((((&("" +phiX174 1430 C 10 .......... $$$$$$$$$" +phiX174 1431 G 10 .......... ########## +phiX174 1432 T 10 .......... """""""""" +phiX174 1433 A 10 .......... ########## +phiX174 1434 C 10 .......... ((((((&(%$ +phiX174 1435 C 10 .......... $$$$$$$$$$ +phiX174 1436 G 10 .......... ########## +phiX174 1437 A 10 .......... """""""""! +phiX174 1438 G 10 .......... """""####! +phiX174 1439 G 10 .......... """""""""! +phiX174 1440 C 10 .......... """""""""! +phiX174 1441 T 10 .......... """"""""#! +phiX174 1442 A 10 .......... $$$%%%&&%! +phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! +phiX174 1444 C 10 **.*...... &%"!"""""! +phiX174 1445 C 10 .......... &%&!%%%&%! +phiX174 1446 C 10 .......... """!"""""! +phiX174 1447 T 10 .$..$....... #"#!"""""! +phiX174 1448 A 8 .$..$..... #!#%%$$! +phiX174 1449 A 6 .$.$.... !""""! +phiX174 1450 T 4 .$... """! +phiX174 1451 G 3 .$.. #"! +phiX174 1452 A 2 .$. "! +phiX174 1453 G 1 .$ !
Binary file samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools/mpileup/samtools_mpileup_out_2.bcf has changed
Binary file samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_in_1.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_1.log Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_1.pileup Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,43 @@ +phiX174 1411 A 0 1 +phiX174 1412 G 0 2,1,1 +phiX174 1413 C 0 3,2,2,1,1 +phiX174 1414 G 0 4,3,3,2,2,1 +phiX174 1415 C 0 5,4,4,3,3,2,1 +phiX174 1416 C 0 6,5,5,4,4,3,2,1 +phiX174 1417 G 0 7,6,6,5,5,4,3,2,1 +phiX174 1418 T 0 8,7,7,6,6,5,4,3,2,1 +phiX174 1419 G 0 9,8,8,7,7,6,5,4,3,2 +phiX174 1420 G 0 10,9,9,8,8,7,6,5,4,3 +phiX174 1421 A 0 11,10,10,9,9,8,7,6,5,4 +phiX174 1422 T 0 12,11,11,10,10,9,8,7,6,5 +phiX174 1423 G 0 13,12,12,11,11,10,9,8,7,6 +phiX174 1424 C 0 14,13,13,12,12,11,10,9,8,7 +phiX174 1425 C 0 15,14,14,13,13,12,11,10,9,8 +phiX174 1426 T 0 16,15,15,14,14,13,12,11,10,9 +phiX174 1427 G 0 17,16,16,15,15,14,13,12,11,10 +phiX174 1428 A 0 18,17,17,16,16,15,14,13,12,11 +phiX174 1429 C 0 19,18,18,17,17,16,15,14,13,12 +phiX174 1430 C 0 20,19,19,18,18,17,16,15,14,13 +phiX174 1431 G 0 21,20,20,19,19,18,17,16,15,14 +phiX174 1432 T 0 22,21,21,20,20,19,18,17,16,15 +phiX174 1433 A 0 23,22,22,21,21,20,19,18,17,16 +phiX174 1434 C 0 24,23,23,22,22,21,20,19,18,17 +phiX174 1435 C 0 25,24,24,23,23,22,21,20,19,18 +phiX174 1436 G 0 26,25,25,24,24,23,22,21,20,19 +phiX174 1437 A 0 27,26,26,25,25,24,23,22,21,20 +phiX174 1438 G 0 28,27,27,26,26,25,24,23,22,21 +phiX174 1439 G 0 29,28,28,27,27,26,25,24,23,22 +phiX174 1440 C 0 30,29,29,28,28,27,26,25,24,23 +phiX174 1441 T 0 31,30,30,29,29,28,27,26,25,24 +phiX174 1442 A 0 32,31,31,30,30,29,28,27,26,25 +phiX174 1443 A 0 33,32,32,31,31,30,29,28,27,26 +phiX174 1444 C 0 34,33,33,32,32,31,30,29,28,27 +phiX174 1445 C 0 34,33,34,32,33,32,31,30,29,28 +phiX174 1446 C 0 35,34,35,33,34,33,32,31,30,29 +phiX174 1447 T 0 36,35,36,34,35,34,33,32,31,30 +phiX174 1448 A 0 36,35,36,35,34,33,32,31 +phiX174 1449 A 0 36,36,35,34,33,32 +phiX174 1450 T 0 36,35,34,33 +phiX174 1451 G 0 36,35,34 +phiX174 1452 A 0 36,35 +phiX174 1453 G 0 36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_2.log Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_2.vcf Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,22 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##samtoolsVersion=1.1+htslib-1.1 +##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat +##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat +##contig=<ID=phiX174,length=5386> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> +##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_3.log Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,2 @@ +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_4.log Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,2 @@ +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/test-data/samtools_mpileup_out_4.vcf Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,22 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##samtoolsVersion=1.1+htslib-1.1 +##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa -C 0 -d 200 -E -q 0 -Q 43 -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_756.dat /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat +##reference=file:///var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa +##contig=<ID=phiX174,length=5386> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> +##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/tool-data/fasta_indexes.loc.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/tool_data_table_conf.xml.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_mpileup/aa0ef6f0ee89/samtools_mpileup/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_reheader/020e144b5f78/samtools_reheader/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_reheader/020e144b5f78/samtools_reheader/samtools_reheader.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,32 @@ +<tool id="samtools_reheader" name="Reheader" version="2.0"> + <description>copy SAM/BAM header between datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> + <inputs> + <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/> + <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/> + </inputs> + <outputs> + <data format="bam" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input_header" ftype="bam" value="reheader_input_header.bam"/> + <param name="input_file" ftype="bam" value="reheader_input_file.bam"/> + <output name="output" ftype="bam" file="reheader_out.bam"/> + </test> + </tests> + <help> +**What it does** + +Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command. + + </help> + <expand macro="citations"></expand> +</tool> +
Binary file samtools/samtools_reheader/020e144b5f78/samtools_reheader/test-data/reheader_input_file.bam has changed
Binary file samtools/samtools_reheader/020e144b5f78/samtools_reheader/test-data/reheader_input_header.bam has changed
Binary file samtools/samtools_reheader/020e144b5f78/samtools_reheader/test-data/reheader_out.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_reheader/020e144b5f78/samtools_reheader/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_rmdup/fe83e6f8e65e/samtools_rmdup/samtools_rmdup.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,69 @@ +<tool id="samtools_rmdup" name="rmdup" version="1.0.1"> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <description>remove PCR duplicates</description> + <command>samtools rmdup + #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE" + ${bam_paired_end_type.force_se} + #else: + -s + #end if + "$input1" "$output1" + 2>&1 || echo "Error running samtools rmdup." >&2 + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File" /> + + <conditional name="bam_paired_end_type"> + <param name="bam_paired_end_type_selector" type="select" label="Is data paired-end"> + <option value="PE" selected="True">BAM is paired-end</option> + <option value="SE">BAM is single-end</option> + </param> + <when value="PE"> + <param name="force_se" type="boolean" label="Treat as single-end" help="(-S)" truevalue="-S" falsevalue="" checked="False"/> + </when> + <when value="SE" /> <!-- No extra parameters here --> + </conditional> + + </inputs> + <outputs> + <data name="output1" format="bam" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <param name="bam_paired_end_type_selector" value="SE" /> + <output name="output1" file="1.bam" ftype="bam" sort="True"/> + </test> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <param name="bam_paired_end_type_selector" value="PE" /> + <param name="force_se" value="True" /> + <output name="output1" file="1.bam" ftype="bam" sort="True"/> + </test> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <param name="bam_paired_end_type_selector" value="PE" /> + <param name="force_se" /> + <output name="output1" file="1.bam" ftype="bam" sort="True" /> + </test> + </tests> + <help> + +**What it does** + +This tool uses the SAMTools_ toolkit to remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_rmdup/fe83e6f8e65e/samtools_rmdup/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_slice_bam/2b474ebbfc7d/samtools_slice_bam/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_slice_bam/2b474ebbfc7d/samtools_slice_bam/samtools_slice_bam.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,123 @@ +<tool id="samtools_slice_bam" name="Slice" version="2.0"> + <description>BAM by genomic regions</description> + <macros> + <import>macros.xml</import> + </macros> + <!-- <code file="samtools_slice_options.py"/> --> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command> +<![CDATA[ + ln -s "${input_bam}" temp_input.bam && + ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai && + + #if str($slice_method.slice_method_selector) == "bed": + + samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && + + #elif str($slice_method.slice_method_selector) == "chr": + + samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam + ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } && + + #elif str($slice_method.slice_method_selector) == "man": + + samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam + + #for $region in $slice_method.regions: + "${region.chrom}:${region.start}-${region.end}" + #end for + + && + + #end if + + samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "${output_bam}" unsorted_output.bam +]]> + </command> + <inputs> + <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" /> + <conditional name="slice_method"> + <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?"> + <option value="bed">using a list of intervals from a BED dataset</option> + <option value="chr">by chromosomes/contigs present in the BAM dataset</option> + <option value="man">by chromosomes/contigs and coordinates</option> + </param> + <when value="bed"> + <param format="bed" label="BED file" name="input_interval" type="data" help="BED datasets can be obtained using "Get Data -> UCSC Main" datasource."/> + </when> + <when value="chr"> + <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below."> + + <!-- The options tagset below extracts reference names from bam file metadata --> + <!-- This will not work with bed files with old style metadata. However this --> + <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking --> + <!-- The pencil icon and settind datatype to "bam" --> + <!-- This change has been commited in the following pull request: --> + <!-- https://github.com/galaxyproject/galaxy/pull/107 --> + + <options> + <filter type="data_meta" ref="input_bam" key="reference_names" /> + </options> + </param> + </when> + <when value="man"> + <repeat name="regions" title="Regions" min="1"> + <param name="chrom" type="select" optional="False" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Select chromosome/contig from the list. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below."> + + <!-- See comments above --> + + <options> + <filter type="data_meta" ref="input_bam" key="reference_names" /> + </options> + </param> + <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/> + <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/> + </repeat> + + + </when> + </conditional> + + </inputs> + <outputs> + <data format="bam" name="output_bam" /> + </outputs> + <tests> + <test> + <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="slice_method_selector" value="bed"/> + <param ftype="bed" name="input_interval" value="bam-slice.bed" /> + <output file="bam-slice-test1.bam" ftype="bam" name="output_bam" /> + </test> + <test> + <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="slice_method_selector" value="chr"/> + <param name="refs" value="chrM" /> + <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" /> + </test> + <test> + <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="slice_method_selector" value="man"/> + <param name="chrom" value="chrM" /> + <param name="start" value="1" /> + <param name="end" value="1000" /> + <output file="bam-slice-test3.bam" ftype="bam" name="output_bam" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**. + +This tool is based on ``samtools view`` command. + +@no-chrom-options@ + +]]> + </help> + <expand macro="citations"></expand> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_slice_bam/2b474ebbfc7d/samtools_slice_bam/test-data/bam-slice.bed Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,38 @@ +chrM 5 1000 myInterval 0 + +chrM 577 647 TRNF 0 + +chrM 648 1601 RNR1 0 + +chrM 1602 1670 TRNV 0 + +chrM 1671 3229 RNR2 0 + +chrM 3230 3304 TRNL1 0 + +chrM 3307 4262 ND1 0 + +chrM 4263 4331 TRNI 0 + +chrM 4329 4400 TRNQ 0 - +chrM 4402 4469 TRNM 0 + +chrM 4470 5511 ND2 0 + +chrM 5512 5579 TRNW 0 + +chrM 5587 5655 TRNA 0 - +chrM 5657 5729 TRNN 0 - +chrM 5761 5826 TRNC 0 - +chrM 5826 5891 TRNY 0 - +chrM 5904 7445 COX1 0 + +chrM 7446 7514 TRNS1 0 - +chrM 7518 7585 TRND 0 + +chrM 7586 8269 COX2 0 + +chrM 8295 8364 TRNK 0 + +chrM 8366 8572 ATP8 0 + +chrM 8527 9207 ATP6 0 + +chrM 9207 9990 COX3 0 + +chrM 9991 10058 TRNG 0 + +chrM 10059 10404 ND3 0 + +chrM 10405 10469 TRNR 0 + +chrM 10470 10766 ND4L 0 + +chrM 10760 12137 ND4 0 + +chrM 12138 12206 TRNH 0 + +chrM 12207 12265 TRNS2 0 + +chrM 12266 12336 TRNL2 0 + +chrM 12337 14148 ND5 0 + +chrM 14149 14673 ND6 0 - +chrM 14674 14742 TRNE 0 - +chrM 14747 15887 CYTB 0 + +chrM 15888 15953 TRNT 0 + +chrM 15956 16023 TRNP 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_slice_bam/2b474ebbfc7d/samtools_slice_bam/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_sort/a430da4f04cd/samtools_sort/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_sort/a430da4f04cd/samtools_sort/samtools_sort.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,40 @@ +<tool id="samtools_sort" name="Sort" version="2.0"> + <description>BAM dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File" /> + <param name="sort_mode" type="select" label="Sort by "> + <option value="" selected="True">Chromosomal coordinates</option> + <option value="-n">Read names (-n)</option> + </param> + </inputs> + <outputs> + <data name="output1" format="bam" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/> + </test> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <param name="sort_mode" value="-n"/> + <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/> + </test> + </tests> + <help> + +**What it does** + +This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. + + + </help> + <expand macro="citations"></expand> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_sort/a430da4f04cd/samtools_sort/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_split/57f3e32f809d/samtools_split/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_split/57f3e32f809d/samtools_split/samtools_split.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,47 @@ +<tool id="samtools_split" name="Split" version="1.1"> + <description>BAM dataset on readgroups</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[ + samtools split -f 'Read_Group_%!.bam' + #if $header: + -u "${output}":"${header}" + #else: + -u "${output}" + #end if + "${input_bam}" + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" /> + </inputs> + <outputs> + <data format="bam" name="output" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" /> + </data> + </outputs> + <tests> + <test> + <param name="input_bam" value="phiX.bam" ftype="bam" /> + <output name="output" file="samtools_split_out.bam"> + <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" /> + <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" /> + <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" /> + </output> + </test> + </tests> + <help> +**What it does** + +Splits BAM files on readgroups. + +This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. + + </help> + <expand macro="citations"></expand> +</tool> +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_split/57f3e32f809d/samtools_split/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/macros.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/samtools_stats.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,296 @@ +<tool id="samtools_stats" name="Stats" version="2.0"> + <description>generate statistics for BAM dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[ + #if $use_reference.use_ref_selector == "yes": + #if $use_reference.reference_source.reference_source_selector == "history": + ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats + #else: + samtools stats + #end if + #else: + samtools stats + #end if + "${input_file}" + --coverage ${coverage_min},${coverage_max},${coverage_step} + ${remove_dups} + #if str( $filter_by_flags.filter_flags ) == "filter": + #if $filter_by_flags.require_flags: + --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])} + #end if + #if $filter_by_flags.exclude_flags: + --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])} + #end if + #end if + --GC-depth ${gc_depth} + --insert-size ${insert_size} + + ## The code below is commented out because using -I/--id options causes the following exception + ## Samtools-htslib: init_group_id() header parsing not yet implemented + + ##if str($read_group) != "": + ## -I "${read_group}" + ##end if + + #if str($read_length) != "0": + --read-length "${read_length}" + #end if + --most-inserts ${most_inserts} + --trim-quality ${trim_quality} + #if $use_reference.use_ref_selector == "yes": + #if $use_reference.reference_source.reference_source_selector != "history": + --ref-seq "${use_reference.reference_source.ref_file.fields.path}" + #else: + --ref-seq "${use_reference.reference_source.ref_file}" + #end if + #end if + > "${output}" + #if $split_output.split_output_selector == "yes": + #set outputs_to_split = str($split_output.generate_tables).split(',') + && mkdir split && echo ${split_output.generate_tables} && + + #if 'sn' in $outputs_to_split: + echo "# Summary Numbers\n" > "split/Summary numbers.tab" && + grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi && + #end if + + #if 'ffq' in $outputs_to_split: + echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" && + grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi && + #end if + + #if 'lfq' in $outputs_to_split: + echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" && + grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi && + #end if + + #if 'mpc' in $outputs_to_split: + echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" && + grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi && + #end if + + #if 'gcf' in $outputs_to_split: + echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" && + grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi && + #end if + + #if 'gcl' in $outputs_to_split: + echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" && + grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi && + #end if + + #if 'gcc' in $outputs_to_split: + echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" && + grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi && + #end if + + #if 'is' in $outputs_to_split: + echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" && + grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- >> "split/Insert sizes.tab" ; fi && + #end if + + #if 'rl' in $outputs_to_split: + echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" && + grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- >> "split/Read lengths.tab" ; fi && + #end if + + #if 'id' in $outputs_to_split: + echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" && + grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- >> "split/Indel distribution.tab" ; fi && + #end if + + #if 'ic' in $outputs_to_split: + echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" && + grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- >> "split/Indels per cycle.tab" ; fi && + #end if + + #if 'cov' in $outputs_to_split: + echo "# Coverage distribution" > "split/Coverage distribution.tab" && + grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi && + #end if + + #if 'gcd' in $outputs_to_split: + echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" && + grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi && + #end if + + ## Unix true command below + + true + + #end if + ]]></command> + <inputs> + <param name="input_file" type="data" format="sam,bam" label="BAM file" /> + <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/> + <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/> + <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/> + <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/> + <conditional name="split_output"> + <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics"> + <option value="no" selected="True">a single summary file</option> + <option value="yes">separate datasets for each statistics</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract"> + <option value="sn">Summary numbers</option> + <option value="ffq">First Fragment Qualities</option> + <option value="lfq">Last Fragment Qualities</option> + <option value="mpc">Mismatches per cycle</option> + <option value="gcf">GC Content of first fragments</option> + <option value="gcl">GC Content of last fragments</option> + <option value="gcc">ACGT content per cycle</option> + <option value="is">Insert sizes</option> + <option value="rl">Read lengths</option> + <option value="id">Indel distribution</option> + <option value="ic">Indels per cycle</option> + <option value="cov">Coverage distribution</option> + <option value="gcd">GC depth</option> + </param> + </when> + </conditional> + <conditional name="filter_by_flags"> + <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options"> + <option value="nofilter" selected="True">Do not filter</option> + <option value="filter">Filter by flags to exclude or require</option> + </param> + <when value="filter"> + <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate 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">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate 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">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + </when> + <when value="nofilter" /> + + </conditional> + <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/> + <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/> + + <!-- + + The -I option of samtools stats returns the following message in version 1.2: + + Samtools-htslib: init_group_id() header parsing not yet implemented + Abort trap: 6 + + Because of this the section below is commented out until this stats bug is fixed + + <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > + <options> + <filter type="data_meta" ref="input_file" key="read_groups" /> + </options> + </param> + + --> + + <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/> + <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/> + <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/> + + <conditional name="use_reference"> + <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation"> + <option value="yes">Use reference</option> + <option selected="True" value="no">Do not use reference</option> + </param> + <when value="yes"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using genome"> + <options from_data_table="fasta_indexes" /> + <filter type="data_meta" ref="input_file" key="dbkey" column="1" /> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using file" /> + </when> + </conditional> + </when> + <when value="no" /> + </conditional> + + </inputs> + + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)\.tab" ext="tabular" visible="true" directory="split" /> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="samtools_stats_input.bam" ftype="bam" /> + <param name="use_ref_selector" value="yes" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> + <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" /> + </test> + <test> + <param name="input_file" value="samtools_stats_input.bam" ftype="bam" /> + <param name="use_ref_selector" value="yes" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> + <param name="split_output_selector" value="yes" /> + <param name="generate_tables" value="sn,mpc,gcc" /> + <output name="output" file="samtools_stats_out2.tab" lines_diff="4"> + <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" /> + <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" /> + <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" /> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool runs the ``samtools stats`` command. It has the following options:: + + -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1] + -d, --remove-dups Exclude from statistics reads marked as duplicates + -f, --required-flag <str|int> Required flag, 0 for unset. See also `samtools flags` [0] + -F, --filtering-flag <str|int> Filtering flag, 0 for unset. See also `samtools flags` [0] + --GC-depth <float> the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4] + -h, --help This help message + -i, --insert-size <int> Maximum insert size [8000] + -I, --id <string> Include only listed read group or sample name + -l, --read-length <int> Include in the statistics only reads with the given read length [] + -m, --most-inserts <float> Report only the main part of inserts [0.99] + -q, --trim-quality <int> The BWA trimming parameter [0] + -r, --ref-seq <file> Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy + will provide options for selecting a reference cached as this Galaxy instance or choosing + one from history. + + + ]]></help> + <expand macro="citations"></expand> +</tool> +
Binary file samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_input.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_out1.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1137 @@ +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1bd20fd8 58ad2167 29883386 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3 2 0 20 38 32 1 0 0 0 0 0 0 +FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 18 36 36 6 0 0 0 0 0 0 +FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 14 31 46 5 0 0 0 0 0 0 +FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 36 42 11 0 0 0 0 0 0 +FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 12 35 43 6 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 7 8 0 0 81 0 0 0 0 +FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 13 1 0 76 0 0 0 0 +FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 11 15 4 0 69 0 0 0 0 +FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 6 20 3 0 68 0 0 0 0 +FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 11 5 0 75 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 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0 +LFQ 243 0 0 0 0 0 0 0 0 0 0 0 0 2 2 17 14 0 0 0 0 0 0 0 0 6 5 5 0 0 0 0 0 6 13 0 2 3 25 0 0 0 0 +LFQ 244 0 0 0 0 0 0 0 0 0 0 0 0 1 3 18 11 0 0 0 0 0 0 0 0 6 5 5 1 0 0 1 0 2 12 0 5 1 29 0 0 0 0 +LFQ 245 0 0 0 0 0 0 0 0 0 0 0 0 1 8 14 11 0 0 0 0 0 0 0 0 8 5 3 1 0 0 1 0 1 15 1 1 3 27 0 0 0 0 +LFQ 246 0 0 0 0 0 0 0 0 0 0 0 0 4 6 15 12 0 0 0 0 0 0 0 0 5 2 8 1 0 1 1 0 1 13 0 2 1 28 0 0 0 0 +LFQ 247 0 0 0 0 0 0 0 0 0 0 0 0 8 3 16 14 0 0 0 0 0 0 0 0 10 4 6 0 0 0 0 0 2 15 1 2 2 17 0 0 0 0 +LFQ 248 0 0 0 0 0 0 0 0 0 0 0 0 5 6 21 8 0 0 0 0 0 0 0 0 7 8 6 2 0 0 0 1 1 14 0 2 2 17 0 0 0 0 +LFQ 249 0 0 0 0 0 0 0 0 0 0 0 0 5 6 20 8 0 0 0 0 0 0 0 0 5 7 10 0 1 0 0 0 1 15 0 2 0 20 0 0 0 0 +LFQ 250 0 0 0 0 0 0 0 0 0 0 0 0 2 10 15 10 0 0 0 0 0 0 0 0 9 5 8 1 0 0 0 2 6 10 0 0 2 20 0 0 0 0 +LFQ 251 0 0 0 0 0 0 0 0 0 0 0 0 7 20 21 17 0 0 0 0 0 0 0 0 7 7 6 0 0 0 0 1 2 4 0 0 0 8 0 0 0 0 +LFQ 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 174 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 175 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 176 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 177 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 178 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +MPC 179 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 +MPC 180 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 181 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 182 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 183 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 184 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 185 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 186 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 187 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 188 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 189 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 190 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 192 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 195 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 196 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 197 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 198 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 199 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 203 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 204 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 205 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 206 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 207 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 208 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 209 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 210 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 211 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 212 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 213 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 214 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 215 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 216 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 217 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 218 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 219 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 220 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 221 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 222 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 223 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 224 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 226 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 227 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 228 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 229 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 230 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 231 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 232 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +MPC 233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 234 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 235 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 236 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 237 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 238 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 239 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 240 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 242 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 243 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 244 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 245 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 246 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 247 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 +MPC 248 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 21.50 29.50 33.50 15.50 +GCC 2 30.00 16.00 11.00 43.00 +GCC 3 33.00 25.00 9.00 33.00 +GCC 4 17.00 29.00 13.00 41.00 +GCC 5 37.00 22.00 12.00 29.00 +GCC 6 36.00 26.00 17.00 21.00 +GCC 7 29.50 13.50 31.50 25.50 +GCC 8 50.50 14.50 19.50 15.50 +GCC 9 17.00 33.00 18.00 32.00 +GCC 10 37.00 14.00 21.00 28.00 +GCC 11 20.50 14.50 29.50 35.50 +GCC 12 30.00 24.00 22.00 24.00 +GCC 13 27.00 15.00 21.00 37.00 +GCC 14 24.00 22.00 26.00 28.00 +GCC 15 25.50 20.50 24.50 29.50 +GCC 16 31.00 15.00 20.00 34.00 +GCC 17 28.00 25.00 14.00 33.00 +GCC 18 30.50 28.50 19.50 21.50 +GCC 19 29.00 26.00 21.00 24.00 +GCC 20 22.50 23.50 17.50 36.50 +GCC 21 35.50 17.50 19.50 27.50 +GCC 22 37.50 28.50 15.50 18.50 +GCC 23 31.00 19.00 13.00 37.00 +GCC 24 37.00 12.00 22.00 29.00 +GCC 25 35.50 22.50 17.50 24.50 +GCC 26 33.50 18.50 15.50 32.50 +GCC 27 34.50 14.50 25.50 25.50 +GCC 28 31.00 14.00 24.00 31.00 +GCC 29 30.00 27.00 24.00 19.00 +GCC 30 31.00 20.00 14.00 35.00 +GCC 31 33.50 29.50 13.50 23.50 +GCC 32 42.50 20.50 19.50 17.50 +GCC 33 25.50 23.50 14.50 36.50 +GCC 34 39.50 16.50 20.50 23.50 +GCC 35 32.50 23.50 21.50 22.50 +GCC 36 42.00 25.00 16.00 17.00 +GCC 37 38.00 17.00 19.00 26.00 +GCC 38 24.00 26.00 25.00 25.00 +GCC 39 22.50 41.50 18.50 17.50 +GCC 40 32.00 16.00 21.00 31.00 +GCC 41 33.00 28.00 19.00 20.00 +GCC 42 30.50 25.50 19.50 24.50 +GCC 43 35.00 29.00 15.00 21.00 +GCC 44 20.00 27.00 22.00 31.00 +GCC 45 40.50 21.50 21.50 16.50 +GCC 46 26.50 20.50 22.50 30.50 +GCC 47 38.50 29.50 16.50 15.50 +GCC 48 27.50 24.50 17.50 30.50 +GCC 49 28.50 32.50 10.50 28.50 +GCC 50 46.50 20.50 9.50 23.50 +GCC 51 34.50 28.50 13.50 23.50 +GCC 52 41.50 23.50 20.50 14.50 +GCC 53 20.00 28.00 26.00 26.00 +GCC 54 31.50 18.50 24.50 25.50 +GCC 55 30.50 22.50 16.50 30.50 +GCC 56 33.50 22.50 13.50 30.50 +GCC 57 23.00 24.00 23.00 30.00 +GCC 58 25.00 37.00 19.00 19.00 +GCC 59 34.00 23.00 24.00 19.00 +GCC 60 29.00 28.00 17.00 26.00 +GCC 61 25.50 23.50 24.50 26.50 +GCC 62 31.50 22.50 16.50 29.50 +GCC 63 27.50 28.50 25.50 18.50 +GCC 64 33.50 21.50 25.50 19.50 +GCC 65 35.50 19.50 18.50 26.50 +GCC 66 34.00 25.00 15.00 26.00 +GCC 67 37.00 23.00 19.00 21.00 +GCC 68 36.50 29.50 13.50 20.50 +GCC 69 38.50 19.50 20.50 21.50 +GCC 70 38.50 16.50 18.50 26.50 +GCC 71 25.50 38.50 21.50 14.50 +GCC 72 29.00 29.00 25.00 17.00 +GCC 73 32.50 20.50 21.50 25.50 +GCC 74 28.50 32.50 12.50 26.50 +GCC 75 41.50 12.50 18.50 27.50 +GCC 76 24.50 29.50 23.50 22.50 +GCC 77 36.00 21.00 18.00 25.00 +GCC 78 27.00 34.00 22.00 17.00 +GCC 79 21.50 26.50 25.50 26.50 +GCC 80 34.00 19.00 28.00 19.00 +GCC 81 17.00 26.00 26.00 31.00 +GCC 82 31.00 30.00 23.00 16.00 +GCC 83 31.50 26.50 12.50 29.50 +GCC 84 19.00 41.00 21.00 19.00 +GCC 85 37.50 24.50 16.50 21.50 +GCC 86 15.00 48.00 15.00 22.00 +GCC 87 41.00 16.00 18.00 25.00 +GCC 88 23.50 27.50 27.50 21.50 +GCC 89 26.50 27.50 26.50 19.50 +GCC 90 18.50 23.50 24.50 33.50 +GCC 91 27.00 32.00 22.00 19.00 +GCC 92 23.50 17.50 27.50 31.50 +GCC 93 25.50 37.50 15.50 21.50 +GCC 94 27.00 17.00 24.00 32.00 +GCC 95 26.50 37.50 14.50 21.50 +GCC 96 29.50 25.50 16.50 28.50 +GCC 97 29.00 31.00 21.00 19.00 +GCC 98 18.00 33.00 22.00 27.00 +GCC 99 24.50 33.50 24.50 17.50 +GCC 100 24.50 16.50 24.50 34.50 +GCC 101 25.00 40.00 19.00 16.00 +GCC 102 17.50 17.50 32.50 32.50 +GCC 103 31.00 26.00 16.00 27.00 +GCC 104 26.50 29.50 20.50 23.50 +GCC 105 34.00 33.00 21.00 12.00 +GCC 106 23.00 31.00 26.00 20.00 +GCC 107 17.50 35.50 23.50 23.50 +GCC 108 24.50 30.50 23.50 21.50 +GCC 109 17.00 31.00 22.00 30.00 +GCC 110 16.00 35.00 24.00 25.00 +GCC 111 24.00 32.00 23.00 21.00 +GCC 112 37.00 28.00 16.00 19.00 +GCC 113 19.50 22.50 32.50 25.50 +GCC 114 17.00 31.00 35.00 17.00 +GCC 115 29.50 24.50 23.50 22.50 +GCC 116 22.00 30.00 34.00 14.00 +GCC 117 27.00 23.00 19.00 31.00 +GCC 118 25.50 14.50 34.50 25.50 +GCC 119 22.50 34.50 20.50 22.50 +GCC 120 17.50 24.50 26.50 31.50 +GCC 121 27.50 33.50 22.50 16.50 +GCC 122 17.00 23.00 25.00 35.00 +GCC 123 23.50 46.50 11.50 18.50 +GCC 124 9.00 32.00 34.00 25.00 +GCC 125 24.00 27.00 19.00 30.00 +GCC 126 26.00 17.00 28.00 29.00 +GCC 127 26.50 16.50 21.50 35.50 +GCC 128 18.00 34.00 31.00 17.00 +GCC 129 25.50 25.50 27.50 21.50 +GCC 130 25.00 20.00 22.00 33.00 +GCC 131 17.50 39.50 24.50 18.50 +GCC 132 21.00 28.00 23.00 28.00 +GCC 133 13.50 31.50 35.50 19.50 +GCC 134 24.50 19.50 30.50 25.50 +GCC 135 16.50 23.50 30.50 29.50 +GCC 136 28.00 32.00 15.00 25.00 +GCC 137 22.50 21.50 30.50 25.50 +GCC 138 14.50 34.50 24.50 26.50 +GCC 139 20.50 29.50 24.50 25.50 +GCC 140 17.00 23.00 30.00 30.00 +GCC 141 20.50 23.50 25.50 30.50 +GCC 142 18.00 29.00 38.00 15.00 +GCC 143 22.00 24.00 27.00 27.00 +GCC 144 21.50 30.50 26.50 21.50 +GCC 145 22.00 21.00 29.00 28.00 +GCC 146 25.00 16.00 39.00 20.00 +GCC 147 26.50 22.50 30.50 20.50 +GCC 148 12.50 28.50 36.50 22.50 +GCC 149 26.50 23.50 23.50 26.50 +GCC 150 14.00 29.00 24.00 33.00 +GCC 151 19.50 30.50 32.50 17.50 +GCC 152 18.50 17.50 29.50 34.50 +GCC 153 22.50 22.50 31.50 23.50 +GCC 154 22.00 21.00 29.00 28.00 +GCC 155 21.00 26.00 19.00 34.00 +GCC 156 14.50 23.50 35.50 26.50 +GCC 157 22.00 31.00 23.00 24.00 +GCC 158 22.50 29.50 24.50 23.50 +GCC 159 17.50 12.50 46.50 23.50 +GCC 160 24.50 26.50 26.50 22.50 +GCC 161 13.00 23.00 45.00 19.00 +GCC 162 31.50 16.50 22.50 29.50 +GCC 163 19.50 21.50 35.50 23.50 +GCC 164 29.00 18.00 21.00 32.00 +GCC 165 14.50 17.50 35.50 32.50 +GCC 166 17.50 37.50 28.50 16.50 +GCC 167 16.50 21.50 31.50 30.50 +GCC 168 14.00 25.00 30.00 31.00 +GCC 169 18.50 20.50 23.50 37.50 +GCC 170 19.00 23.00 28.00 30.00 +GCC 171 20.00 28.00 33.00 19.00 +GCC 172 19.00 20.00 32.00 29.00 +GCC 173 24.50 16.50 33.50 25.50 +GCC 174 17.50 23.50 33.50 25.50 +GCC 175 33.50 17.50 35.50 13.50 +GCC 176 16.50 32.50 28.50 22.50 +GCC 177 19.00 22.00 27.00 32.00 +GCC 178 16.00 26.00 30.00 28.00 +GCC 179 18.00 18.00 22.00 42.00 +GCC 180 21.00 22.00 34.00 23.00 +GCC 181 20.50 19.50 35.50 24.50 +GCC 182 32.50 18.50 22.50 26.50 +GCC 183 24.50 13.50 28.50 33.50 +GCC 184 15.00 29.00 30.00 26.00 +GCC 185 15.00 32.00 33.00 20.00 +GCC 186 22.50 23.50 34.50 19.50 +GCC 187 19.00 14.00 40.00 27.00 +GCC 188 27.50 21.50 27.50 23.50 +GCC 189 17.00 22.00 34.00 27.00 +GCC 190 23.00 30.00 23.00 24.00 +GCC 191 25.00 22.00 28.00 25.00 +GCC 192 34.50 24.50 13.50 27.50 +GCC 193 18.50 25.50 25.50 30.50 +GCC 194 18.50 33.50 24.50 23.50 +GCC 195 16.00 26.00 23.00 35.00 +GCC 196 21.50 25.50 24.50 28.50 +GCC 197 20.00 21.00 23.00 36.00 +GCC 198 17.00 21.00 37.00 25.00 +GCC 199 20.50 18.50 25.50 35.50 +GCC 200 21.00 29.00 21.00 29.00 +GCC 201 27.00 21.00 23.00 29.00 +GCC 202 21.50 24.50 19.50 34.50 +GCC 203 21.50 24.50 26.50 27.50 +GCC 204 27.00 29.00 24.00 20.00 +GCC 205 19.50 21.50 22.50 36.50 +GCC 206 26.50 24.50 21.50 27.50 +GCC 207 22.50 21.50 19.50 36.50 +GCC 208 14.00 35.00 29.00 22.00 +GCC 209 16.00 23.00 12.00 49.00 +GCC 210 18.50 19.50 40.50 21.50 +GCC 211 26.00 20.00 22.00 32.00 +GCC 212 21.00 31.00 18.00 30.00 +GCC 213 24.00 15.00 31.00 30.00 +GCC 214 17.50 24.50 25.50 32.50 +GCC 215 26.00 24.00 23.00 27.00 +GCC 216 21.50 17.50 25.50 35.50 +GCC 217 26.00 29.00 17.00 28.00 +GCC 218 20.00 27.00 21.00 32.00 +GCC 219 17.00 21.00 21.00 41.00 +GCC 220 25.50 23.50 23.50 27.50 +GCC 221 21.50 23.50 20.50 34.50 +GCC 222 21.50 21.50 18.50 38.50 +GCC 223 20.00 27.00 28.00 25.00 +GCC 224 22.50 22.50 24.50 30.50 +GCC 225 14.50 35.50 30.50 19.50 +GCC 226 20.00 23.00 26.00 31.00 +GCC 227 20.50 24.50 23.50 31.50 +GCC 228 33.00 19.00 26.00 22.00 +GCC 229 22.50 24.50 18.50 34.50 +GCC 230 21.00 32.00 16.00 31.00 +GCC 231 23.00 28.00 30.00 19.00 +GCC 232 23.50 21.50 12.50 42.50 +GCC 233 21.00 27.00 25.00 27.00 +GCC 234 16.50 27.50 22.50 33.50 +GCC 235 20.00 15.00 28.00 37.00 +GCC 236 28.00 23.00 21.00 28.00 +GCC 237 20.50 19.50 22.50 37.50 +GCC 238 21.50 29.50 24.50 24.50 +GCC 239 20.00 8.00 17.00 55.00 +GCC 240 28.00 24.00 16.00 32.00 +GCC 241 22.50 22.50 16.50 38.50 +GCC 242 29.00 25.00 13.00 33.00 +GCC 243 22.50 15.50 23.50 38.50 +GCC 244 20.50 23.50 16.50 39.50 +GCC 245 28.00 23.00 19.00 30.00 +GCC 246 21.00 29.00 25.00 25.00 +GCC 247 32.00 14.00 13.00 41.00 +GCC 248 18.00 18.00 25.00 39.00 +GCC 249 25.00 23.00 21.00 31.00 +GCC 250 27.50 22.50 17.50 32.50 +GCC 251 13.50 20.50 36.50 29.50 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 251 200 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_out2.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,1137 @@ +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1bd20fd8 58ad2167 29883386 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 200 +SN filtered sequences: 0 +SN sequences: 200 +SN is sorted: 1 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 200 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 6 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3 2 0 20 38 32 1 0 0 0 0 0 0 +FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 18 36 36 6 0 0 0 0 0 0 +FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 14 31 46 5 0 0 0 0 0 0 +FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 36 42 11 0 0 0 0 0 0 +FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 12 35 43 6 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 7 8 0 0 81 0 0 0 0 +FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 13 1 0 76 0 0 0 0 +FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 11 15 4 0 69 0 0 0 0 +FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 6 20 3 0 68 0 0 0 0 +FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 11 5 0 75 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 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0 +LFQ 243 0 0 0 0 0 0 0 0 0 0 0 0 2 2 17 14 0 0 0 0 0 0 0 0 6 5 5 0 0 0 0 0 6 13 0 2 3 25 0 0 0 0 +LFQ 244 0 0 0 0 0 0 0 0 0 0 0 0 1 3 18 11 0 0 0 0 0 0 0 0 6 5 5 1 0 0 1 0 2 12 0 5 1 29 0 0 0 0 +LFQ 245 0 0 0 0 0 0 0 0 0 0 0 0 1 8 14 11 0 0 0 0 0 0 0 0 8 5 3 1 0 0 1 0 1 15 1 1 3 27 0 0 0 0 +LFQ 246 0 0 0 0 0 0 0 0 0 0 0 0 4 6 15 12 0 0 0 0 0 0 0 0 5 2 8 1 0 1 1 0 1 13 0 2 1 28 0 0 0 0 +LFQ 247 0 0 0 0 0 0 0 0 0 0 0 0 8 3 16 14 0 0 0 0 0 0 0 0 10 4 6 0 0 0 0 0 2 15 1 2 2 17 0 0 0 0 +LFQ 248 0 0 0 0 0 0 0 0 0 0 0 0 5 6 21 8 0 0 0 0 0 0 0 0 7 8 6 2 0 0 0 1 1 14 0 2 2 17 0 0 0 0 +LFQ 249 0 0 0 0 0 0 0 0 0 0 0 0 5 6 20 8 0 0 0 0 0 0 0 0 5 7 10 0 1 0 0 0 1 15 0 2 0 20 0 0 0 0 +LFQ 250 0 0 0 0 0 0 0 0 0 0 0 0 2 10 15 10 0 0 0 0 0 0 0 0 9 5 8 1 0 0 0 2 6 10 0 0 2 20 0 0 0 0 +LFQ 251 0 0 0 0 0 0 0 0 0 0 0 0 7 20 21 17 0 0 0 0 0 0 0 0 7 7 6 0 0 0 0 1 2 4 0 0 0 8 0 0 0 0 +LFQ 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. First column is the cycle number, second +# is the number of N's and the rest is the number of mismatches +MPC 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +MPC 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 +MPC 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 +MPC 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +MPC 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 206 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 207 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 208 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 209 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 210 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 211 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 212 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 213 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 214 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 215 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 216 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 217 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 218 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 219 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 220 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 221 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 222 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 223 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 224 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 226 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 227 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 228 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 229 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 230 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 231 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 232 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +MPC 233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 234 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 235 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 236 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 237 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 238 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 239 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 240 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 242 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 243 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 244 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 245 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 246 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 247 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 +MPC 248 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 21.50 29.50 33.50 15.50 +GCC 2 30.00 16.00 11.00 43.00 +GCC 3 33.00 25.00 9.00 33.00 +GCC 4 17.00 29.00 13.00 41.00 +GCC 5 37.00 22.00 12.00 29.00 +GCC 6 36.00 26.00 17.00 21.00 +GCC 7 29.50 13.50 31.50 25.50 +GCC 8 50.50 14.50 19.50 15.50 +GCC 9 17.00 33.00 18.00 32.00 +GCC 10 37.00 14.00 21.00 28.00 +GCC 11 20.50 14.50 29.50 35.50 +GCC 12 30.00 24.00 22.00 24.00 +GCC 13 27.00 15.00 21.00 37.00 +GCC 14 24.00 22.00 26.00 28.00 +GCC 15 25.50 20.50 24.50 29.50 +GCC 16 31.00 15.00 20.00 34.00 +GCC 17 28.00 25.00 14.00 33.00 +GCC 18 30.50 28.50 19.50 21.50 +GCC 19 29.00 26.00 21.00 24.00 +GCC 20 22.50 23.50 17.50 36.50 +GCC 21 35.50 17.50 19.50 27.50 +GCC 22 37.50 28.50 15.50 18.50 +GCC 23 31.00 19.00 13.00 37.00 +GCC 24 37.00 12.00 22.00 29.00 +GCC 25 35.50 22.50 17.50 24.50 +GCC 26 33.50 18.50 15.50 32.50 +GCC 27 34.50 14.50 25.50 25.50 +GCC 28 31.00 14.00 24.00 31.00 +GCC 29 30.00 27.00 24.00 19.00 +GCC 30 31.00 20.00 14.00 35.00 +GCC 31 33.50 29.50 13.50 23.50 +GCC 32 42.50 20.50 19.50 17.50 +GCC 33 25.50 23.50 14.50 36.50 +GCC 34 39.50 16.50 20.50 23.50 +GCC 35 32.50 23.50 21.50 22.50 +GCC 36 42.00 25.00 16.00 17.00 +GCC 37 38.00 17.00 19.00 26.00 +GCC 38 24.00 26.00 25.00 25.00 +GCC 39 22.50 41.50 18.50 17.50 +GCC 40 32.00 16.00 21.00 31.00 +GCC 41 33.00 28.00 19.00 20.00 +GCC 42 30.50 25.50 19.50 24.50 +GCC 43 35.00 29.00 15.00 21.00 +GCC 44 20.00 27.00 22.00 31.00 +GCC 45 40.50 21.50 21.50 16.50 +GCC 46 26.50 20.50 22.50 30.50 +GCC 47 38.50 29.50 16.50 15.50 +GCC 48 27.50 24.50 17.50 30.50 +GCC 49 28.50 32.50 10.50 28.50 +GCC 50 46.50 20.50 9.50 23.50 +GCC 51 34.50 28.50 13.50 23.50 +GCC 52 41.50 23.50 20.50 14.50 +GCC 53 20.00 28.00 26.00 26.00 +GCC 54 31.50 18.50 24.50 25.50 +GCC 55 30.50 22.50 16.50 30.50 +GCC 56 33.50 22.50 13.50 30.50 +GCC 57 23.00 24.00 23.00 30.00 +GCC 58 25.00 37.00 19.00 19.00 +GCC 59 34.00 23.00 24.00 19.00 +GCC 60 29.00 28.00 17.00 26.00 +GCC 61 25.50 23.50 24.50 26.50 +GCC 62 31.50 22.50 16.50 29.50 +GCC 63 27.50 28.50 25.50 18.50 +GCC 64 33.50 21.50 25.50 19.50 +GCC 65 35.50 19.50 18.50 26.50 +GCC 66 34.00 25.00 15.00 26.00 +GCC 67 37.00 23.00 19.00 21.00 +GCC 68 36.50 29.50 13.50 20.50 +GCC 69 38.50 19.50 20.50 21.50 +GCC 70 38.50 16.50 18.50 26.50 +GCC 71 25.50 38.50 21.50 14.50 +GCC 72 29.00 29.00 25.00 17.00 +GCC 73 32.50 20.50 21.50 25.50 +GCC 74 28.50 32.50 12.50 26.50 +GCC 75 41.50 12.50 18.50 27.50 +GCC 76 24.50 29.50 23.50 22.50 +GCC 77 36.00 21.00 18.00 25.00 +GCC 78 27.00 34.00 22.00 17.00 +GCC 79 21.50 26.50 25.50 26.50 +GCC 80 34.00 19.00 28.00 19.00 +GCC 81 17.00 26.00 26.00 31.00 +GCC 82 31.00 30.00 23.00 16.00 +GCC 83 31.50 26.50 12.50 29.50 +GCC 84 19.00 41.00 21.00 19.00 +GCC 85 37.50 24.50 16.50 21.50 +GCC 86 15.00 48.00 15.00 22.00 +GCC 87 41.00 16.00 18.00 25.00 +GCC 88 23.50 27.50 27.50 21.50 +GCC 89 26.50 27.50 26.50 19.50 +GCC 90 18.50 23.50 24.50 33.50 +GCC 91 27.00 32.00 22.00 19.00 +GCC 92 23.50 17.50 27.50 31.50 +GCC 93 25.50 37.50 15.50 21.50 +GCC 94 27.00 17.00 24.00 32.00 +GCC 95 26.50 37.50 14.50 21.50 +GCC 96 29.50 25.50 16.50 28.50 +GCC 97 29.00 31.00 21.00 19.00 +GCC 98 18.00 33.00 22.00 27.00 +GCC 99 24.50 33.50 24.50 17.50 +GCC 100 24.50 16.50 24.50 34.50 +GCC 101 25.00 40.00 19.00 16.00 +GCC 102 17.50 17.50 32.50 32.50 +GCC 103 31.00 26.00 16.00 27.00 +GCC 104 26.50 29.50 20.50 23.50 +GCC 105 34.00 33.00 21.00 12.00 +GCC 106 23.00 31.00 26.00 20.00 +GCC 107 17.50 35.50 23.50 23.50 +GCC 108 24.50 30.50 23.50 21.50 +GCC 109 17.00 31.00 22.00 30.00 +GCC 110 16.00 35.00 24.00 25.00 +GCC 111 24.00 32.00 23.00 21.00 +GCC 112 37.00 28.00 16.00 19.00 +GCC 113 19.50 22.50 32.50 25.50 +GCC 114 17.00 31.00 35.00 17.00 +GCC 115 29.50 24.50 23.50 22.50 +GCC 116 22.00 30.00 34.00 14.00 +GCC 117 27.00 23.00 19.00 31.00 +GCC 118 25.50 14.50 34.50 25.50 +GCC 119 22.50 34.50 20.50 22.50 +GCC 120 17.50 24.50 26.50 31.50 +GCC 121 27.50 33.50 22.50 16.50 +GCC 122 17.00 23.00 25.00 35.00 +GCC 123 23.50 46.50 11.50 18.50 +GCC 124 9.00 32.00 34.00 25.00 +GCC 125 24.00 27.00 19.00 30.00 +GCC 126 26.00 17.00 28.00 29.00 +GCC 127 26.50 16.50 21.50 35.50 +GCC 128 18.00 34.00 31.00 17.00 +GCC 129 25.50 25.50 27.50 21.50 +GCC 130 25.00 20.00 22.00 33.00 +GCC 131 17.50 39.50 24.50 18.50 +GCC 132 21.00 28.00 23.00 28.00 +GCC 133 13.50 31.50 35.50 19.50 +GCC 134 24.50 19.50 30.50 25.50 +GCC 135 16.50 23.50 30.50 29.50 +GCC 136 28.00 32.00 15.00 25.00 +GCC 137 22.50 21.50 30.50 25.50 +GCC 138 14.50 34.50 24.50 26.50 +GCC 139 20.50 29.50 24.50 25.50 +GCC 140 17.00 23.00 30.00 30.00 +GCC 141 20.50 23.50 25.50 30.50 +GCC 142 18.00 29.00 38.00 15.00 +GCC 143 22.00 24.00 27.00 27.00 +GCC 144 21.50 30.50 26.50 21.50 +GCC 145 22.00 21.00 29.00 28.00 +GCC 146 25.00 16.00 39.00 20.00 +GCC 147 26.50 22.50 30.50 20.50 +GCC 148 12.50 28.50 36.50 22.50 +GCC 149 26.50 23.50 23.50 26.50 +GCC 150 14.00 29.00 24.00 33.00 +GCC 151 19.50 30.50 32.50 17.50 +GCC 152 18.50 17.50 29.50 34.50 +GCC 153 22.50 22.50 31.50 23.50 +GCC 154 22.00 21.00 29.00 28.00 +GCC 155 21.00 26.00 19.00 34.00 +GCC 156 14.50 23.50 35.50 26.50 +GCC 157 22.00 31.00 23.00 24.00 +GCC 158 22.50 29.50 24.50 23.50 +GCC 159 17.50 12.50 46.50 23.50 +GCC 160 24.50 26.50 26.50 22.50 +GCC 161 13.00 23.00 45.00 19.00 +GCC 162 31.50 16.50 22.50 29.50 +GCC 163 19.50 21.50 35.50 23.50 +GCC 164 29.00 18.00 21.00 32.00 +GCC 165 14.50 17.50 35.50 32.50 +GCC 166 17.50 37.50 28.50 16.50 +GCC 167 16.50 21.50 31.50 30.50 +GCC 168 14.00 25.00 30.00 31.00 +GCC 169 18.50 20.50 23.50 37.50 +GCC 170 19.00 23.00 28.00 30.00 +GCC 171 20.00 28.00 33.00 19.00 +GCC 172 19.00 20.00 32.00 29.00 +GCC 173 24.50 16.50 33.50 25.50 +GCC 174 17.50 23.50 33.50 25.50 +GCC 175 33.50 17.50 35.50 13.50 +GCC 176 16.50 32.50 28.50 22.50 +GCC 177 19.00 22.00 27.00 32.00 +GCC 178 16.00 26.00 30.00 28.00 +GCC 179 18.00 18.00 22.00 42.00 +GCC 180 21.00 22.00 34.00 23.00 +GCC 181 20.50 19.50 35.50 24.50 +GCC 182 32.50 18.50 22.50 26.50 +GCC 183 24.50 13.50 28.50 33.50 +GCC 184 15.00 29.00 30.00 26.00 +GCC 185 15.00 32.00 33.00 20.00 +GCC 186 22.50 23.50 34.50 19.50 +GCC 187 19.00 14.00 40.00 27.00 +GCC 188 27.50 21.50 27.50 23.50 +GCC 189 17.00 22.00 34.00 27.00 +GCC 190 23.00 30.00 23.00 24.00 +GCC 191 25.00 22.00 28.00 25.00 +GCC 192 34.50 24.50 13.50 27.50 +GCC 193 18.50 25.50 25.50 30.50 +GCC 194 18.50 33.50 24.50 23.50 +GCC 195 16.00 26.00 23.00 35.00 +GCC 196 21.50 25.50 24.50 28.50 +GCC 197 20.00 21.00 23.00 36.00 +GCC 198 17.00 21.00 37.00 25.00 +GCC 199 20.50 18.50 25.50 35.50 +GCC 200 21.00 29.00 21.00 29.00 +GCC 201 27.00 21.00 23.00 29.00 +GCC 202 21.50 24.50 19.50 34.50 +GCC 203 21.50 24.50 26.50 27.50 +GCC 204 27.00 29.00 24.00 20.00 +GCC 205 19.50 21.50 22.50 36.50 +GCC 206 26.50 24.50 21.50 27.50 +GCC 207 22.50 21.50 19.50 36.50 +GCC 208 14.00 35.00 29.00 22.00 +GCC 209 16.00 23.00 12.00 49.00 +GCC 210 18.50 19.50 40.50 21.50 +GCC 211 26.00 20.00 22.00 32.00 +GCC 212 21.00 31.00 18.00 30.00 +GCC 213 24.00 15.00 31.00 30.00 +GCC 214 17.50 24.50 25.50 32.50 +GCC 215 26.00 24.00 23.00 27.00 +GCC 216 21.50 17.50 25.50 35.50 +GCC 217 26.00 29.00 17.00 28.00 +GCC 218 20.00 27.00 21.00 32.00 +GCC 219 17.00 21.00 21.00 41.00 +GCC 220 25.50 23.50 23.50 27.50 +GCC 221 21.50 23.50 20.50 34.50 +GCC 222 21.50 21.50 18.50 38.50 +GCC 223 20.00 27.00 28.00 25.00 +GCC 224 22.50 22.50 24.50 30.50 +GCC 225 14.50 35.50 30.50 19.50 +GCC 226 20.00 23.00 26.00 31.00 +GCC 227 20.50 24.50 23.50 31.50 +GCC 228 33.00 19.00 26.00 22.00 +GCC 229 22.50 24.50 18.50 34.50 +GCC 230 21.00 32.00 16.00 31.00 +GCC 231 23.00 28.00 30.00 19.00 +GCC 232 23.50 21.50 12.50 42.50 +GCC 233 21.00 27.00 25.00 27.00 +GCC 234 16.50 27.50 22.50 33.50 +GCC 235 20.00 15.00 28.00 37.00 +GCC 236 28.00 23.00 21.00 28.00 +GCC 237 20.50 19.50 22.50 37.50 +GCC 238 21.50 29.50 24.50 24.50 +GCC 239 20.00 8.00 17.00 55.00 +GCC 240 28.00 24.00 16.00 32.00 +GCC 241 22.50 22.50 16.50 38.50 +GCC 242 29.00 25.00 13.00 33.00 +GCC 243 22.50 15.50 23.50 38.50 +GCC 244 20.50 23.50 16.50 39.50 +GCC 245 28.00 23.00 19.00 30.00 +GCC 246 21.00 29.00 25.00 25.00 +GCC 247 32.00 14.00 13.00 41.00 +GCC 248 18.00 18.00 25.00 39.00 +GCC 249 25.00 23.00 21.00 31.00 +GCC 250 27.50 22.50 17.50 32.50 +GCC 251 13.50 20.50 36.50 29.50 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 251 200 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_out2/gcc.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,252 @@ +# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent) +1 21.50 29.50 33.50 15.50 +2 30.00 16.00 11.00 43.00 +3 33.00 25.00 9.00 33.00 +4 17.00 29.00 13.00 41.00 +5 37.00 22.00 12.00 29.00 +6 36.00 26.00 17.00 21.00 +7 29.50 13.50 31.50 25.50 +8 50.50 14.50 19.50 15.50 +9 17.00 33.00 18.00 32.00 +10 37.00 14.00 21.00 28.00 +11 20.50 14.50 29.50 35.50 +12 30.00 24.00 22.00 24.00 +13 27.00 15.00 21.00 37.00 +14 24.00 22.00 26.00 28.00 +15 25.50 20.50 24.50 29.50 +16 31.00 15.00 20.00 34.00 +17 28.00 25.00 14.00 33.00 +18 30.50 28.50 19.50 21.50 +19 29.00 26.00 21.00 24.00 +20 22.50 23.50 17.50 36.50 +21 35.50 17.50 19.50 27.50 +22 37.50 28.50 15.50 18.50 +23 31.00 19.00 13.00 37.00 +24 37.00 12.00 22.00 29.00 +25 35.50 22.50 17.50 24.50 +26 33.50 18.50 15.50 32.50 +27 34.50 14.50 25.50 25.50 +28 31.00 14.00 24.00 31.00 +29 30.00 27.00 24.00 19.00 +30 31.00 20.00 14.00 35.00 +31 33.50 29.50 13.50 23.50 +32 42.50 20.50 19.50 17.50 +33 25.50 23.50 14.50 36.50 +34 39.50 16.50 20.50 23.50 +35 32.50 23.50 21.50 22.50 +36 42.00 25.00 16.00 17.00 +37 38.00 17.00 19.00 26.00 +38 24.00 26.00 25.00 25.00 +39 22.50 41.50 18.50 17.50 +40 32.00 16.00 21.00 31.00 +41 33.00 28.00 19.00 20.00 +42 30.50 25.50 19.50 24.50 +43 35.00 29.00 15.00 21.00 +44 20.00 27.00 22.00 31.00 +45 40.50 21.50 21.50 16.50 +46 26.50 20.50 22.50 30.50 +47 38.50 29.50 16.50 15.50 +48 27.50 24.50 17.50 30.50 +49 28.50 32.50 10.50 28.50 +50 46.50 20.50 9.50 23.50 +51 34.50 28.50 13.50 23.50 +52 41.50 23.50 20.50 14.50 +53 20.00 28.00 26.00 26.00 +54 31.50 18.50 24.50 25.50 +55 30.50 22.50 16.50 30.50 +56 33.50 22.50 13.50 30.50 +57 23.00 24.00 23.00 30.00 +58 25.00 37.00 19.00 19.00 +59 34.00 23.00 24.00 19.00 +60 29.00 28.00 17.00 26.00 +61 25.50 23.50 24.50 26.50 +62 31.50 22.50 16.50 29.50 +63 27.50 28.50 25.50 18.50 +64 33.50 21.50 25.50 19.50 +65 35.50 19.50 18.50 26.50 +66 34.00 25.00 15.00 26.00 +67 37.00 23.00 19.00 21.00 +68 36.50 29.50 13.50 20.50 +69 38.50 19.50 20.50 21.50 +70 38.50 16.50 18.50 26.50 +71 25.50 38.50 21.50 14.50 +72 29.00 29.00 25.00 17.00 +73 32.50 20.50 21.50 25.50 +74 28.50 32.50 12.50 26.50 +75 41.50 12.50 18.50 27.50 +76 24.50 29.50 23.50 22.50 +77 36.00 21.00 18.00 25.00 +78 27.00 34.00 22.00 17.00 +79 21.50 26.50 25.50 26.50 +80 34.00 19.00 28.00 19.00 +81 17.00 26.00 26.00 31.00 +82 31.00 30.00 23.00 16.00 +83 31.50 26.50 12.50 29.50 +84 19.00 41.00 21.00 19.00 +85 37.50 24.50 16.50 21.50 +86 15.00 48.00 15.00 22.00 +87 41.00 16.00 18.00 25.00 +88 23.50 27.50 27.50 21.50 +89 26.50 27.50 26.50 19.50 +90 18.50 23.50 24.50 33.50 +91 27.00 32.00 22.00 19.00 +92 23.50 17.50 27.50 31.50 +93 25.50 37.50 15.50 21.50 +94 27.00 17.00 24.00 32.00 +95 26.50 37.50 14.50 21.50 +96 29.50 25.50 16.50 28.50 +97 29.00 31.00 21.00 19.00 +98 18.00 33.00 22.00 27.00 +99 24.50 33.50 24.50 17.50 +100 24.50 16.50 24.50 34.50 +101 25.00 40.00 19.00 16.00 +102 17.50 17.50 32.50 32.50 +103 31.00 26.00 16.00 27.00 +104 26.50 29.50 20.50 23.50 +105 34.00 33.00 21.00 12.00 +106 23.00 31.00 26.00 20.00 +107 17.50 35.50 23.50 23.50 +108 24.50 30.50 23.50 21.50 +109 17.00 31.00 22.00 30.00 +110 16.00 35.00 24.00 25.00 +111 24.00 32.00 23.00 21.00 +112 37.00 28.00 16.00 19.00 +113 19.50 22.50 32.50 25.50 +114 17.00 31.00 35.00 17.00 +115 29.50 24.50 23.50 22.50 +116 22.00 30.00 34.00 14.00 +117 27.00 23.00 19.00 31.00 +118 25.50 14.50 34.50 25.50 +119 22.50 34.50 20.50 22.50 +120 17.50 24.50 26.50 31.50 +121 27.50 33.50 22.50 16.50 +122 17.00 23.00 25.00 35.00 +123 23.50 46.50 11.50 18.50 +124 9.00 32.00 34.00 25.00 +125 24.00 27.00 19.00 30.00 +126 26.00 17.00 28.00 29.00 +127 26.50 16.50 21.50 35.50 +128 18.00 34.00 31.00 17.00 +129 25.50 25.50 27.50 21.50 +130 25.00 20.00 22.00 33.00 +131 17.50 39.50 24.50 18.50 +132 21.00 28.00 23.00 28.00 +133 13.50 31.50 35.50 19.50 +134 24.50 19.50 30.50 25.50 +135 16.50 23.50 30.50 29.50 +136 28.00 32.00 15.00 25.00 +137 22.50 21.50 30.50 25.50 +138 14.50 34.50 24.50 26.50 +139 20.50 29.50 24.50 25.50 +140 17.00 23.00 30.00 30.00 +141 20.50 23.50 25.50 30.50 +142 18.00 29.00 38.00 15.00 +143 22.00 24.00 27.00 27.00 +144 21.50 30.50 26.50 21.50 +145 22.00 21.00 29.00 28.00 +146 25.00 16.00 39.00 20.00 +147 26.50 22.50 30.50 20.50 +148 12.50 28.50 36.50 22.50 +149 26.50 23.50 23.50 26.50 +150 14.00 29.00 24.00 33.00 +151 19.50 30.50 32.50 17.50 +152 18.50 17.50 29.50 34.50 +153 22.50 22.50 31.50 23.50 +154 22.00 21.00 29.00 28.00 +155 21.00 26.00 19.00 34.00 +156 14.50 23.50 35.50 26.50 +157 22.00 31.00 23.00 24.00 +158 22.50 29.50 24.50 23.50 +159 17.50 12.50 46.50 23.50 +160 24.50 26.50 26.50 22.50 +161 13.00 23.00 45.00 19.00 +162 31.50 16.50 22.50 29.50 +163 19.50 21.50 35.50 23.50 +164 29.00 18.00 21.00 32.00 +165 14.50 17.50 35.50 32.50 +166 17.50 37.50 28.50 16.50 +167 16.50 21.50 31.50 30.50 +168 14.00 25.00 30.00 31.00 +169 18.50 20.50 23.50 37.50 +170 19.00 23.00 28.00 30.00 +171 20.00 28.00 33.00 19.00 +172 19.00 20.00 32.00 29.00 +173 24.50 16.50 33.50 25.50 +174 17.50 23.50 33.50 25.50 +175 33.50 17.50 35.50 13.50 +176 16.50 32.50 28.50 22.50 +177 19.00 22.00 27.00 32.00 +178 16.00 26.00 30.00 28.00 +179 18.00 18.00 22.00 42.00 +180 21.00 22.00 34.00 23.00 +181 20.50 19.50 35.50 24.50 +182 32.50 18.50 22.50 26.50 +183 24.50 13.50 28.50 33.50 +184 15.00 29.00 30.00 26.00 +185 15.00 32.00 33.00 20.00 +186 22.50 23.50 34.50 19.50 +187 19.00 14.00 40.00 27.00 +188 27.50 21.50 27.50 23.50 +189 17.00 22.00 34.00 27.00 +190 23.00 30.00 23.00 24.00 +191 25.00 22.00 28.00 25.00 +192 34.50 24.50 13.50 27.50 +193 18.50 25.50 25.50 30.50 +194 18.50 33.50 24.50 23.50 +195 16.00 26.00 23.00 35.00 +196 21.50 25.50 24.50 28.50 +197 20.00 21.00 23.00 36.00 +198 17.00 21.00 37.00 25.00 +199 20.50 18.50 25.50 35.50 +200 21.00 29.00 21.00 29.00 +201 27.00 21.00 23.00 29.00 +202 21.50 24.50 19.50 34.50 +203 21.50 24.50 26.50 27.50 +204 27.00 29.00 24.00 20.00 +205 19.50 21.50 22.50 36.50 +206 26.50 24.50 21.50 27.50 +207 22.50 21.50 19.50 36.50 +208 14.00 35.00 29.00 22.00 +209 16.00 23.00 12.00 49.00 +210 18.50 19.50 40.50 21.50 +211 26.00 20.00 22.00 32.00 +212 21.00 31.00 18.00 30.00 +213 24.00 15.00 31.00 30.00 +214 17.50 24.50 25.50 32.50 +215 26.00 24.00 23.00 27.00 +216 21.50 17.50 25.50 35.50 +217 26.00 29.00 17.00 28.00 +218 20.00 27.00 21.00 32.00 +219 17.00 21.00 21.00 41.00 +220 25.50 23.50 23.50 27.50 +221 21.50 23.50 20.50 34.50 +222 21.50 21.50 18.50 38.50 +223 20.00 27.00 28.00 25.00 +224 22.50 22.50 24.50 30.50 +225 14.50 35.50 30.50 19.50 +226 20.00 23.00 26.00 31.00 +227 20.50 24.50 23.50 31.50 +228 33.00 19.00 26.00 22.00 +229 22.50 24.50 18.50 34.50 +230 21.00 32.00 16.00 31.00 +231 23.00 28.00 30.00 19.00 +232 23.50 21.50 12.50 42.50 +233 21.00 27.00 25.00 27.00 +234 16.50 27.50 22.50 33.50 +235 20.00 15.00 28.00 37.00 +236 28.00 23.00 21.00 28.00 +237 20.50 19.50 22.50 37.50 +238 21.50 29.50 24.50 24.50 +239 20.00 8.00 17.00 55.00 +240 28.00 24.00 16.00 32.00 +241 22.50 22.50 16.50 38.50 +242 29.00 25.00 13.00 33.00 +243 22.50 15.50 23.50 38.50 +244 20.50 23.50 16.50 39.50 +245 28.00 23.00 19.00 30.00 +246 21.00 29.00 25.00 25.00 +247 32.00 14.00 13.00 41.00 +248 18.00 18.00 25.00 39.00 +249 25.00 23.00 21.00 31.00 +250 27.50 22.50 17.50 32.50 +251 13.50 20.50 36.50 29.50
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_out2/mpc.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,253 @@ +# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches +1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_out2/sn.tab Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,33 @@ +# Summary Numbers + +raw total sequences: 200 +filtered sequences: 0 +sequences: 200 +is sorted: 1 +1st fragments: 100 +last fragments: 100 +reads mapped: 25 +reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +reads unmapped: 175 +reads properly paired: 0 # proper-pair bit set +reads paired: 200 # paired-end technology bit set +reads duplicated: 0 # PCR or optical duplicate bit set +reads MQ0: 6 # mapped and MQ=0 +reads QC failed: 0 +non-primary alignments: 0 +total length: 50200 # ignores clipping +bases mapped: 6275 # ignores clipping +bases mapped (cigar): 6275 # more accurate +bases trimmed: 0 +bases duplicated: 0 +mismatches: 591 # from NM fields +error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +average length: 251 +maximum length: 251 +average quality: 34.7 +insert size average: 0.0 +insert size standard deviation: 0.0 +inward oriented pairs: 0 +outward oriented pairs: 0 +pairs with other orientation: 0 +pairs on different chromosomes: 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/test-data/samtools_stats_ref.fa Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,239 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/tool-data/fasta_indexes.loc.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/tool_data_table_conf.xml.sample Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/samtools_stats/8cfc17e27132/samtools_stats/tool_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/suite_samtools_1_2/5b673ccc8747/suite_samtools_1_2/repository_dependencies.xml Fri Oct 04 07:01:45 2019 -0400 @@ -0,0 +1,17 @@ +<?xml version="1.0"?> +<repositories description="A suite of Galaxy tools designed to work with version 1.2 of the SAMtools package."> + <repository changeset_revision="cf875cbe2df4" name="data_manager_sam_fasta_index_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="af7c50162f0b" name="bam_to_sam" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d04d9f1c6791" name="sam_to_bam" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="8c3472790020" name="samtools_bedcov" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1ebb4ecdc1ef" name="samtools_calmd" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0072bf593791" name="samtools_flagstat" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="87398ae795c7" name="samtools_idxstats" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c6fdfe3331d6" name="samtools_mpileup" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="020e144b5f78" name="samtools_reheader" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3735f950b2f5" name="samtools_rmdup" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2b474ebbfc7d" name="samtools_slice_bam" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a430da4f04cd" name="samtools_sort" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="57f3e32f809d" name="samtools_split" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0d71d9467847" name="samtools_stats" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>