| Previous changeset 7:bfc4517aa037 (2015-11-11) Next changeset 9:fa7ad9b89f4a (2018-09-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
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modified:
macros.xml samtools_mpileup.xml test-data/samtools_mpileup_out_1.pileup test-data/samtools_mpileup_out_2.vcf |
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added:
test-data/samtools_mpileup_out_3.pileup |
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removed:
test-data/samtools/mpileup/samtools_mpileup_out_1.log test-data/samtools/mpileup/samtools_mpileup_out_1.pileup test-data/samtools/mpileup/samtools_mpileup_out_2.bcf test-data/samtools_mpileup_out_1.log test-data/samtools_mpileup_out_2.log test-data/samtools_mpileup_out_3.log test-data/samtools_mpileup_out_4.log tool_dependencies.xml |
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| diff -r bfc4517aa037 -r 583abf29fc8e macros.xml --- a/macros.xml Wed Nov 11 12:53:32 2015 -0500 +++ b/macros.xml Tue May 09 11:17:20 2017 -0400 |
| [ |
| @@ -1,16 +1,17 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <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},} + url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 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> |
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| diff -r bfc4517aa037 -r 583abf29fc8e samtools_mpileup.xml --- a/samtools_mpileup.xml Wed Nov 11 12:53:32 2015 -0500 +++ b/samtools_mpileup.xml Tue May 09 11:17:20 2017 -0400 |
| [ |
| b'@@ -1,25 +1,30 @@\n-<tool id="samtools_mpileup" name="MPileup" version="2.1.1">\n- <description>call variants</description>\n+<tool id="samtools_mpileup" name="MPileup" version="2.1.3">\n+ <description>multi-way pileup of variants</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements" />\n <expand macro="stdio" />\n <expand macro="version_command" />\n- <command>\n- <![CDATA[\n+ <command><![CDATA[\n+ #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):\n+ ln -s \'${input_bam}\' \'localbam_${bam_count}.bam\' &&\n+ ln -s \'${input_bam.metadata.bam_index}\' \'localbam_${bam_count}.bam.bai\' &&\n+ #end for\n+\n #if $reference_source.reference_source_selector == "history":\n- ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup\n- #else:\n- samtools mpileup\n+ ln -s \'${reference_source.ref_file}\' &&\n+ samtools faidx `basename \'${reference_source.ref_file}\'` &&\n #end if\n+\n+ samtools mpileup\n #if $reference_source.reference_source_selector != "history":\n- -f "${reference_source.ref_file.fields.path}"\n+ -f \'${reference_source.ref_file.fields.path}\'\n #else:\n- -f "${reference_source.ref_file}"\n+ -f \'${reference_source.ref_file}\'\n #end if\n- #for $bam in $reference_source.input_bam:\n- "${bam}"\n+ #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):\n+ localbam_${bam_count}.bam\n #end for\n #if str( $advanced_options.advanced_options_selector ) == "advanced":\n #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":\n@@ -31,95 +36,110 @@\n #end if\n #end if\n #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":\n- -l "$pasted_regions"\n+ -l \'$pasted_regions\'\n #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"\n- -l "$advanced_options.limit_by_region.bed_regions"\n+ -l \'$advanced_options.limit_by_region.bed_regions\'\n #end if\n #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":\n- -G "$excluded_read_groups"\n+ -G \'$excluded_read_groups\'\n #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"\n- -G "$advanced_options.exclude_read_group.read_groups"\n+ -G \'$advanced_options.exclude_read_group.read_groups\'\n #end if\n ${advanced_options.skip_anomalous_read_pairs}\n ${advanced_options.disable_probabilistic_realignment}\n- -C "${advanced_options.coefficient_for_downgrading}"\n- -d "${advanced_options.max_reads_per_bam}"\n+ -C ${advanced_options.coefficient_for_downgrading}\n+ -d ${advanced_options.max_reads_per_bam}\n ${advanced_options.extended_BAQ_computation}\n- -q "${advanced_options.minimum_mapping_quality}"\n- -Q "${advanced_options.minimum_base_quality}"\n+ -q ${advanced_options.minimum_mapping_quality}\n+ -Q ${advanced_options.minimum_base_quality}\n #if str( $advanced_options.region_string ):\n- -r "${advanced_options.region_string}"\n+ -r \'${advanced_options.region_string}\'\n #end if\n-\n #end if\n #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == \'perform_genotype_likelihood_computation\':\n- ##\n-\n ${genotype_likelihood_computation_type.output_format}\n ${genotype_likelihood_computation_type.compressed}\n \n #if str( $genotype_likelihood_computation_type.output_tags ) != "None":\n- --output-tags "${genotype_likelihood_computation_type.output_tags}"\n+ --output-tags \'${genotype_likelihood_computation_type.output_tags}\'\n #end if\n \n #if str( $genotype_likelihood_computation_type.per'..b's. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.\n-\n-------\n-\n-**Input options**::\n-\n- -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding\n- -A, --count-orphans do not discard anomalous read pairs\n- -b, --bam-list FILE list of input BAM filenames, one per line\n- -B, --no-BAQ disable BAQ (per-Base Alignment Quality)\n- -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]\n- -d, --max-depth INT max per-BAM depth; avoids excessive memory usage [250]\n- -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs\n- -f, --fasta-ref FILE faidx indexed reference sequence file\n- -G, --exclude-RG FILE exclude read groups listed in FILE\n- -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)\n- -q, --min-MQ INT skip alignments with mapQ smaller than INT [0]\n- -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13]\n- -r, --region REG region in which pileup is generated\n- -R, --ignore-RG ignore RG tags (one BAM = one sample)\n- --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset []\n- --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set\n- [UNMAP,SECONDARY,QCFAIL,DUP]\n- -x, --ignore-overlaps disable read-pair overlap detection\n-\n-**Output options**::\n-\n- -o, --output FILE write output to FILE [standard output]\n- -g, --BCF generate genotype likelihoods in BCF format\n- -v, --VCF generate genotype likelihoods in VCF format\n-\n-**Output options for mpileup format** (without -g/-v)::\n-\n- -O, --output-BP output base positions on reads\n- -s, --output-MQ output mapping quality\n-\n-**Output options for genotype likelihoods** (when -g/-v is used)::\n-\n- -t, --output-tags LIST optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP []\n- -u, --uncompressed generate uncompressed VCF/BCF output\n-\n-**SNP/INDEL genotype likelihoods options** (effective with -g/-v)::\n-\n- -e, --ext-prob INT Phred-scaled gap extension seq error probability [20]\n- -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002]\n- -h, --tandem-qual INT coefficient for homopolymer errors [100]\n- -I, --skip-indels do not perform indel calling\n- -L, --max-idepth INT maximum per-sample depth for INDEL calling [250]\n- -m, --min-ireads INT minimum number gapped reads for indel candidates [1]\n- -o, --open-prob INT Phred-scaled gap open seq error probability [40]\n- -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity\n- -P, --platforms STR comma separated list of platforms for indels [all]\n+Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines.\n+If sample identifiers are absent, each input file is regarded as one sample.\n \n **Notes**: Assuming diploid individuals.\n-]]>\n- </help>\n- <configfiles>\n- <configfile name="excluded_read_groups">\n-<![CDATA[\n-#set pasted_data = \'\'\n-#if str( $advanced_options.advanced_options_selector ) == "advanced":\n- #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":\n- #set pasted_data = \'\\t\'.join( str( $advanced_options.exclude_read_group[\'read_groups\'] ).split() )\n- #end if\n-#end if\n-${pasted_data}\n-]]>\n- </configfile>\n- <configfile name="pasted_regions">\n-<![CDATA[\n-#set pasted_data = \'\'\n-#if str( $advanced_options.advanced_options_selector ) == "advanced":\n- #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":\n- #set pasted_data = \'\\t\'.join( str( $advanced_options.limit_by_region[\'region_paste\'] ).split() )\n- #end if\n-#end if\n-${pasted_data}\n-]]>\n- </configfile>\n- </configfiles>\n+ ]]></help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools/mpileup/samtools_mpileup_out_1.log --- a/test-data/samtools/mpileup/samtools_mpileup_out_1.log Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -[mpileup] 1 samples in 1 input files -<mpileup> Set max per-file depth to 8000 |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools/mpileup/samtools_mpileup_out_1.pileup --- a/test-data/samtools/mpileup/samtools_mpileup_out_1.pileup Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,43 +0,0 @@ -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 .$ ! |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools/mpileup/samtools_mpileup_out_2.bcf |
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| Binary file test-data/samtools/mpileup/samtools_mpileup_out_2.bcf has changed |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_1.log --- a/test-data/samtools_mpileup_out_1.log Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -[fai_load] build FASTA index. -[mpileup] 1 samples in 1 input files -<mpileup> Set max per-file depth to 8000 |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_1.pileup --- a/test-data/samtools_mpileup_out_1.pileup Wed Nov 11 12:53:32 2015 -0500 +++ b/test-data/samtools_mpileup_out_1.pileup Tue May 09 11:17:20 2017 -0400 |
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| @@ -1,43 +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 +phiX174 1411 A 0 +phiX174 1412 G 0 +phiX174 1413 C 0 +phiX174 1414 G 0 +phiX174 1415 C 0 +phiX174 1416 C 0 +phiX174 1417 G 0 +phiX174 1418 T 0 +phiX174 1419 G 0 +phiX174 1420 G 0 +phiX174 1421 A 0 +phiX174 1422 T 0 +phiX174 1423 G 0 +phiX174 1424 C 0 +phiX174 1425 C 0 +phiX174 1426 T 0 +phiX174 1427 G 0 +phiX174 1428 A 0 +phiX174 1429 C 0 +phiX174 1430 C 0 +phiX174 1431 G 0 +phiX174 1432 T 0 +phiX174 1433 A 0 +phiX174 1434 C 0 +phiX174 1435 C 0 +phiX174 1436 G 0 +phiX174 1437 A 0 +phiX174 1438 G 0 +phiX174 1439 G 0 +phiX174 1440 C 0 +phiX174 1441 T 0 +phiX174 1442 A 0 +phiX174 1443 A 0 +phiX174 1444 C 0 +phiX174 1445 C 0 +phiX174 1446 C 0 +phiX174 1447 T 0 +phiX174 1448 A 0 +phiX174 1449 A 0 +phiX174 1450 T 0 +phiX174 1451 G 0 +phiX174 1452 A 0 +phiX174 1453 G 0 |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_2.log --- a/test-data/samtools_mpileup_out_2.log Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,3 +0,0 @@ -[fai_load] build FASTA index. -[mpileup] 1 samples in 1 input files -<mpileup> Set max per-file depth to 8000 |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_2.vcf --- a/test-data/samtools_mpileup_out_2.vcf Wed Nov 11 12:53:32 2015 -0500 +++ b/test-data/samtools_mpileup_out_2.vcf Tue May 09 11:17:20 2017 -0400 |
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| @@ -4,7 +4,7 @@ ##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."> +##ALT=<ID=*,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"> @@ -19,4 +19,4 @@ ##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 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_3.log --- a/test-data/samtools_mpileup_out_3.log Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,2 +0,0 @@ -[mpileup] 1 samples in 1 input files -<mpileup> Set max per-file depth to 8000 |
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| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_3.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_3.pileup Tue May 09 11:17:20 2017 -0400 |
| b |
| @@ -0,0 +1,43 @@ +phiX174 1411 A 1 ^P. $ P 1 +phiX174 1412 G 3 .^D.^F. "$$ PDF 2,1,1 +phiX174 1413 C 5 ...^D.^F. """$$ PDFDF 3,2,2,1,1 +phiX174 1414 G 6 .....^F. #####$ PDFDFF 4,3,3,2,2,1 +phiX174 1415 C 7 ......^F. %%%%%%& PDFDFFF 5,4,4,3,3,2,1 +phiX174 1416 C 8 .......^F. $$$$$$$$ PDFDFFFF 6,5,5,4,4,3,2,1 +phiX174 1417 G 9 ........^F. "#######$ PDFDFFFFF 7,6,6,5,5,4,3,2,1 +phiX174 1418 T 10 .........^F. """""""""$ PDFDFFFFFF 8,7,7,6,6,5,4,3,2,1 +phiX174 1419 G 10 .......... """""'&'%$ PDFDFFFFFF 9,8,8,7,7,6,5,4,3,2 +phiX174 1420 G 10 .......... """""""""" PDFDFFFFFF 10,9,9,8,8,7,6,5,4,3 +phiX174 1421 A 10 .......... """""""""" PDFDFFFFFF 11,10,10,9,9,8,7,6,5,4 +phiX174 1422 T 10 .......... """""""""" PDFDFFFFFF 12,11,11,10,10,9,8,7,6,5 +phiX174 1423 G 10 .......... """""""""# PDFDFFFFFF 13,12,12,11,11,10,9,8,7,6 +phiX174 1424 C 10 ..A.AAAAAA %""""""""" PDFDFFFFFF 14,13,13,12,12,11,10,9,8,7 +phiX174 1425 C 10 .......... $$$""""""" PDFDFFFFFF 15,14,14,13,13,12,11,10,9,8 +phiX174 1426 T 10 .......... #####""""" PDFDFFFFFF 16,15,15,14,14,13,12,11,10,9 +phiX174 1427 G 10 .......... ######"""" PDFDFFFFFF 17,16,16,15,15,14,13,12,11,10 +phiX174 1428 A 10 .......... """""""""" PDFDFFFFFF 18,17,17,16,16,15,14,13,12,11 +phiX174 1429 C 10 .......... ((((((&("" PDFDFFFFFF 19,18,18,17,17,16,15,14,13,12 +phiX174 1430 C 10 .......... $$$$$$$$$" PDFDFFFFFF 20,19,19,18,18,17,16,15,14,13 +phiX174 1431 G 10 .......... ########## PDFDFFFFFF 21,20,20,19,19,18,17,16,15,14 +phiX174 1432 T 10 .......... """""""""" PDFDFFFFFF 22,21,21,20,20,19,18,17,16,15 +phiX174 1433 A 10 .......... ########## PDFDFFFFFF 23,22,22,21,21,20,19,18,17,16 +phiX174 1434 C 10 .......... ((((((&(%$ PDFDFFFFFF 24,23,23,22,22,21,20,19,18,17 +phiX174 1435 C 10 .......... $$$$$$$$$$ PDFDFFFFFF 25,24,24,23,23,22,21,20,19,18 +phiX174 1436 G 10 .......... ########## PDFDFFFFFF 26,25,25,24,24,23,22,21,20,19 +phiX174 1437 A 10 .......... """""""""! PDFDFFFFFF 27,26,26,25,25,24,23,22,21,20 +phiX174 1438 G 10 .......... """""####! PDFDFFFFFF 28,27,27,26,26,25,24,23,22,21 +phiX174 1439 G 10 .......... """""""""! PDFDFFFFFF 29,28,28,27,27,26,25,24,23,22 +phiX174 1440 C 10 .......... """""""""! PDFDFFFFFF 30,29,29,28,28,27,26,25,24,23 +phiX174 1441 T 10 .......... """"""""#! PDFDFFFFFF 31,30,30,29,29,28,27,26,25,24 +phiX174 1442 A 10 .......... $$$%%%&&%! PDFDFFFFFF 32,31,31,30,30,29,28,27,26,25 +phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! PDFDFFFFFF 33,32,32,31,31,30,29,28,27,26 +phiX174 1444 C 10 **.*...... !!"!"""""! PDFDFFFFFF 34,33,33,32,32,31,30,29,28,27 +phiX174 1445 C 10 .......... !!&!%%%&%! PDFDFFFFFF 34,33,34,32,33,32,31,30,29,28 +phiX174 1446 C 10 .......... !!"!"""""! PDFDFFFFFF 35,34,35,33,34,33,32,31,30,29 +phiX174 1447 T 10 .$..$....... !!#!"""""! PDFDFFFFFF 36,35,36,34,35,34,33,32,31,30 +phiX174 1448 A 8 .$..$..... !!#%%$$! DDFFFFFF 36,35,36,35,34,33,32,31 +phiX174 1449 A 6 .$.$.... !""""! DFFFFF 36,36,35,34,33,32 +phiX174 1450 T 4 .$... """! FFFF 36,35,34,33 +phiX174 1451 G 3 .$.. #"! FFF 36,35,34 +phiX174 1452 A 2 .$. "! FF 36,35 +phiX174 1453 G 1 .$ ! F 36 |
| b |
| diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_4.log --- a/test-data/samtools_mpileup_out_4.log Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,2 +0,0 @@ -[mpileup] 1 samples in 1 input files -<mpileup> Set max per-file depth to 8000 |
| b |
| diff -r bfc4517aa037 -r 583abf29fc8e tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:53:32 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?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> |