This is an automated email from the git hooks/post-receive script. anton-khodak-guest pushed a commit to branch debian/unstable in repository samtools.
commit 129288348521ba3ad532d4ba24eb3a5ccb74b703 Author: Anton Khodak <[email protected]> Date: Thu Jan 12 00:33:24 2017 -0800 Add CWL tools --- debian/changelog | 6 ++ debian/copyright | 25 ++++- debian/samtools-Dockerfile | 84 +++++++++++++++ debian/samtools-docker.yml | 5 + debian/samtools-faidx.cwl | 78 ++++++++++++++ debian/samtools-index.cwl | 86 +++++++++++++++ debian/samtools-metadata.yaml | 73 +++++++++++++ debian/samtools-rmdup.cwl | 75 +++++++++++++ debian/samtools-sort.cwl | 106 ++++++++++++++++++ debian/samtools-view.cwl | 242 ++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 776 insertions(+), 4 deletions(-) diff --git a/debian/changelog b/debian/changelog index d3a434c..62a2d41 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +samtools (1.3.1-4) unstable; urgency=low + + * CWL files added + + -- Anton Khodak <[email protected]> Fri, 13 Jan 2017 06:27:27 -0800 + samtools (1.3.1-3) unstable; urgency=medium * Team upload. diff --git a/debian/copyright b/debian/copyright index eddbb8c..05fba1c 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz Files: * @@ -7,7 +7,7 @@ Copyright: © 2008–2016, Genome Research Ltd. (GRL) © 2009–2012 Broad Institute © 2010 Illumina, Inc. © 2012–2013 Peter Cock, The James Hutton Institute. -License: MIT +License: Expat Files: win32/xcurses.h win32/libcurses.a Copyright: Public Domain @@ -37,7 +37,25 @@ License: zlib Jean-loup Gailly Mark Adler [email protected] [email protected] -License: MIT +Files: debian/*.cwl +Copyright: the CWL project +License: Apache-2.0 + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + . + http://www.apache.org/licenses/LICENSE-2.0 + . + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + . + On Debian systems, the complete text of the Apache 2.0 License + can be found in /usr/share/common-licenses/Apache-2.0 file. + +License: Expat Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights @@ -55,4 +73,3 @@ License: MIT LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - diff --git a/debian/samtools-Dockerfile b/debian/samtools-Dockerfile new file mode 100644 index 0000000..6f6b755 --- /dev/null +++ b/debian/samtools-Dockerfile @@ -0,0 +1,84 @@ +################################################################# +# Dockerfile +# +# Software: samtools +# Software Version: 1.2-242-4d56437 +# Description: samtools image for SciDAP +# Website: https://samtools.github.io, http://scidap.com/ +# Provides: samtools/htslib/tabix/bgzip +# Base Image: scidap/scidap:v0.0.1 +# Build Cmd: docker build --rm -t scidap/samtools:v1.2-242-4d56437 . +# Pull Cmd: docker pull scidap/samtools:v1.2-242-4d56437 +# Run Cmd: docker run --rm scidap/samtools:v1.2-242-4d56437 samtools +################################################################# + +### Base Image +FROM scidap/scidap:v0.0.1 +MAINTAINER Andrey V Kartashov "[email protected]" +ENV DEBIAN_FRONTEND noninteractive + +################## BEGIN INSTALLATION ###################### + +WORKDIR /tmp + +### Install required packages (samtools) + +RUN apt-get clean all &&\ + apt-get update &&\ + apt-get install -y \ + libncurses5-dev && \ + apt-get clean && \ + apt-get purge && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc/* + +### Installing samtools/htslib/tabix/bgzip + +ENV VERSIONH 1.2.1-254-6462e34 +ENV NAMEH htslib +ENV URLH "https://github.com/samtools/htslib/archive/${VERSIONH}.tar.gz"; +ENV SHA1H "6462e349d16e83db8647272e4b98d2a92992071f" + +ENV VERSION 1.2-242-4d56437 +ENV NAME "samtools" +ENV URL "https://github.com/samtools/samtools/archive/${VERSION}.tar.gz"; +ENV SHA1 "4d56437320ad370eb0b48c204ccec7c73f653393" + +RUN git clone https://github.com/samtools/htslib.git && \ +cd ${NAMEH} && \ +git reset --hard ${SHA1H} && \ +make -j 4 && \ +cd .. && \ +cp ./${NAMEH}/tabix /usr/local/bin/ && \ +cp ./${NAMEH}/bgzip /usr/local/bin/ && \ +cp ./${NAMEH}/htsfile /usr/local/bin/ && \ +#RUN wget -q -O - $URLH | tar -zxv && \ +#cd ${NAMEH}-${VERSIONH} && \ +#make -j 4 && \ +#cd .. && \ +#cp ./${NAMEH}-${VERSIONH}/tabix /usr/local/bin/ && \ +#cp ./${NAMEH}-${VERSIONH}/bgzip /usr/local/bin/ && \ +#cp ./${NAMEH}-${VERSIONH}/htsfile /usr/local/bin/ && \ +strip /usr/local/bin/tabix; true && \ +strip /usr/local/bin/bgzip; true && \ +strip /usr/local/bin/htsfile; true && \ +#ln -s ./${NAMEH}-${VERSIONH}/ ./${NAMEH} && \ + +git clone https://github.com/samtools/samtools.git && \ +cd ${NAME} && \ +git reset --hard ${SHA1} && \ +make -j 4 && \ +cp ./${NAME} /usr/local/bin/ && \ +cd .. && \ +strip /usr/local/bin/${NAME}; true && \ +rm -rf ./${NAMEH}/ && \ +rm -rf ./${NAME}/ && \ +rm -rf ./${NAMEH} + +#wget -q -O - $URL | tar -zxv && \ +#cd ${NAME}-${VERSION} && \ +#make -j 4 && \ +#cd .. && \ +#cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \ +#strip /usr/local/bin/${NAME}; true && \ +#rm -rf ./${NAMEH}-${VERSIONH}/ && \ +#rm -rf ./${NAME}-${VERSION}/ diff --git a/debian/samtools-docker.yml b/debian/samtools-docker.yml new file mode 100644 index 0000000..4f4348e --- /dev/null +++ b/debian/samtools-docker.yml @@ -0,0 +1,5 @@ +class: DockerRequirement +dockerPull: scidap/samtools:v1.2-242-4d56437 +#dockerImageId: scidap/samtools:v1.2-242-4d56437 #not yet ready +dockerFile: > + $import: samtools-Dockerfile diff --git a/debian/samtools-faidx.cwl b/debian/samtools-faidx.cwl new file mode 100755 index 0000000..203c1c0 --- /dev/null +++ b/debian/samtools-faidx.cwl @@ -0,0 +1,78 @@ +#!/usr/bin/env cwl-runner +# +# To use it as stand alone tool. The working directory should not have input .fa file +# example: "./samtools-faidx.cwl --input=./test-files/mm10.fa" +# As part of a workflow should be no problem at all + +cwlVersion: v1.0 +class: CommandLineTool + +requirements: +- $import: envvar-global.yml +- $import: samtools-docker.yml +- class: InlineJavascriptRequirement +- class: InitialWorkDirRequirement + listing: + - entry: $(inputs.input) + entryname: $(inputs.input.path.split('/').slice(-1)[0]) +inputs: + input: + type: File + doc: <file.fa|file.fa.gz> + region: + type: string? + inputBinding: + position: 2 + +outputs: + index: + type: File + outputBinding: + glob: $(inputs.input.path.split('/').slice(-1)[0]) #+'.fai') + secondaryFiles: + - .fai + - .gzi + +baseCommand: +- samtools +- faidx + +arguments: +- valueFrom: $(inputs.input.path.split('/').slice(-1)[0]) + position: 1 + +$namespaces: + s: http://schema.org/ + +$schemas: +- http://schema.org/docs/schema_org_rdfa.html + +s:mainEntity: + $import: samtools-metadata.yaml + +s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-faidx.cwl +s:codeRepository: https://github.com/common-workflow-language/workflows +s:license: http://www.apache.org/licenses/LICENSE-2.0 + +s:isPartOf: + class: s:CreativeWork + s:name: Common Workflow Language + s:url: http://commonwl.org/ + +s:author: + class: s:Person + s:name: Andrey Kartashov + s:email: mailto:[email protected] + s:sameAs: + - id: http://orcid.org/0000-0001-9102-5681 + s:worksFor: + - class: s:Organization + s:name: Cincinnati Children's Hospital Medical Center + s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026 + s:department: + - class: s:Organization + s:name: Barski Lab +doc: | + samtools-faidx.cwl is developed for CWL consortium + Usage: samtools faidx <file.fa|file.fa.gz> [<reg> [...]] + diff --git a/debian/samtools-index.cwl b/debian/samtools-index.cwl new file mode 100755 index 0000000..9bdc5b1 --- /dev/null +++ b/debian/samtools-index.cwl @@ -0,0 +1,86 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: CommandLineTool + +requirements: +- $import: envvar-global.yml +- $import: samtools-docker.yml +- class: InlineJavascriptRequirement + expressionLib: + - var new_ext = function() { var ext=inputs.bai?'.bai':inputs.csi?'.csi':'.bai'; + return inputs.input.path.split('/').slice(-1)[0]+ext; }; +inputs: + input: + type: File + inputBinding: + position: 2 + + doc: | + Input bam file. + interval: + type: int? + inputBinding: + position: 1 + prefix: -m + doc: | + Set minimum interval size for CSI indices to 2^INT [14] + csi: + type: boolean + default: false + doc: | + Generate CSI-format index for BAM files + bai: + type: boolean + default: false + doc: | + Generate BAI-format index for BAM files [default] +outputs: + index: + type: File + outputBinding: + glob: $(new_ext()) + + doc: The index file +baseCommand: [samtools, index] +arguments: +- valueFrom: $(inputs.bai?'-b':inputs.csi?'-c':[]) + position: 1 +- valueFrom: $(new_ext()) + position: 3 + +$namespaces: + s: http://schema.org/ + +$schemas: +- http://schema.org/docs/schema_org_rdfa.html + +s:mainEntity: + $import: samtools-metadata.yaml + +s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-index.cwl +s:codeRepository: https://github.com/common-workflow-language/workflows +s:license: http://www.apache.org/licenses/LICENSE-2.0 + +s:isPartOf: + class: s:CreativeWork + s:name: Common Workflow Language + s:url: http://commonwl.org/ + +s:author: + class: s:Person + s:name: Andrey Kartashov + s:email: mailto:[email protected] + s:sameAs: + - id: http://orcid.org/0000-0001-9102-5681 + s:worksFor: + - class: s:Organization + s:name: Cincinnati Children's Hospital Medical Center + s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026 + s:department: + - class: s:Organization + s:name: Barski Lab +doc: | + samtools-index.cwl is developed for CWL consortium + + diff --git a/debian/samtools-metadata.yaml b/debian/samtools-metadata.yaml new file mode 100644 index 0000000..64b6852 --- /dev/null +++ b/debian/samtools-metadata.yaml @@ -0,0 +1,73 @@ +class: s:SoftwareSourceCode +s:name: "samtools" +s:about: > + A suite of programs for interacting with high-throughput sequencing data. + It consists of three separate repositories: Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format), + BCFtools (Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants) + and HTSlib (A C library for reading/writing high-throughput sequencing data). + +s:url: http://www.htslib.org/ +s:codeRepository: https://github.com/samtools/samtools.git + +s:license: +- https://opensource.org/licenses/MIT +- https://opensource.org/licenses/BSD-3-Clause + +s:targetProduct: + class: s:SoftwareApplication + s:softwareVersion: "1.2-242-4d56437" + s:applicationCategory: "commandline tool" + +s:programmingLanguage: "C, Perl" + +s:publication: +- class: s:ScholarlyArticle + id: http://dx.doi.org/10.1093/bioinformatics/btr509 + s:name: "(Li, 2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics." + s:url: http://www.ncbi.nlm.nih.gov/pubmed/21903627 +- class: s:ScholarlyArticle + id: http://dx.doi.org/10.1093/bioinformatics/btr076 + s:name: "(Li, 2011) Improving SNP discovery by base alignment quality. Bioinformatics." + s:url: http://www.ncbi.nlm.nih.gov/pubmed/21320865 +- class: s:ScholarlyArticle + id: http://dx.doi.org/10.1093/bioinformatics/btp352 + s:name: "(Li et al., 2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics." + s:url: http://www.ncbi.nlm.nih.gov/pubmed/19505943 + +s:discussionUrl: +- https://lists.sourceforge.net/lists/listinfo/samtools-help +- https://lists.sourceforge.net/lists/listinfo/samtools-devel + +s:creator: +- class: s:Organization + s:name: "Sanger Institute" + s:member: + - class: s:Person + s:name: "Heng Li" + s:description: "wrote most of the initial source codes of SAMtools and various converters." +- class: s:Organization + s:name: "Broad Institute" + s:member: + - class: s:Person + s:name: "Bob Handsaker" + s:description: | + A major contributor to the + SAM/BAM specification. He designed and implemented the BGZF format, the + underlying indexable compression format for the BAM format. BGZF does + not support arithmetic between file offsets. +- class: s:Organization + s:name: "Beijing Genome Institute" + s:member: + - class: s:Person + s:name: "Jue Ruan" + s:description: | + Designed and implemented the + RAZF format, an alternative indexable compression format. RAZF is no longer + used by or provided with SAMtools. Source code remains available in older + SAMtools 0.1.x releases and from the standalone branch in the repository. +- class: s:Person + s:name: "Colin Hercus" + s:description: "updated novo2sam.pl to support gapped alignment by novoalign." +- class: s:Person + s:name: "Petr Danecek" + s:description: "contributed the header parsing library sam_header.c and sam2vcf.pl script." \ No newline at end of file diff --git a/debian/samtools-rmdup.cwl b/debian/samtools-rmdup.cwl new file mode 100755 index 0000000..196a8e9 --- /dev/null +++ b/debian/samtools-rmdup.cwl @@ -0,0 +1,75 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: CommandLineTool + +requirements: +- $import: envvar-global.yml +- $import: samtools-docker.yml +- class: InlineJavascriptRequirement + +inputs: + single_end: + type: boolean + default: false + doc: | + rmdup for SE reads + input: + type: File + inputBinding: + position: 2 + + doc: | + Input bam file. + output_name: + type: string + inputBinding: + position: 3 + + pairend_as_se: + type: boolean + default: false + doc: | + treat PE reads as SE in rmdup (force -s) +outputs: + rmdup: + type: File + outputBinding: + glob: $(inputs.output_name) + + doc: File with removed duplicates +baseCommand: [samtools, rmdup] +$namespaces: + s: http://schema.org/ + +$schemas: +- http://schema.org/docs/schema_org_rdfa.html + +s:mainEntity: + $import: samtools-metadata.yaml + +s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-rmdup.cwl +s:codeRepository: https://github.com/common-workflow-language/workflows +s:license: http://www.apache.org/licenses/LICENSE-2.0 + +s:isPartOf: + class: s:CreativeWork + s:name: Common Workflow Language + s:url: http://commonwl.org/ + +s:author: + class: s:Person + s:name: Andrey Kartashov + s:email: mailto:[email protected] + s:sameAs: + - id: http://orcid.org/0000-0001-9102-5681 + s:worksFor: + - class: s:Organization + s:name: Cincinnati Children's Hospital Medical Center + s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026 + s:department: + - class: s:Organization + s:name: Barski Lab +doc: | + samtools-rmdup.cwl is developed for CWL consortium + diff --git a/debian/samtools-sort.cwl b/debian/samtools-sort.cwl new file mode 100755 index 0000000..77b5a85 --- /dev/null +++ b/debian/samtools-sort.cwl @@ -0,0 +1,106 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: CommandLineTool + +requirements: +- $import: envvar-global.yml +- $import: samtools-docker.yml +- class: InlineJavascriptRequirement + +inputs: + compression_level: + type: int? + inputBinding: + prefix: -l + doc: | + Set compression level, from 0 (uncompressed) to 9 (best) + threads: + type: int? + inputBinding: + prefix: -@ + + doc: Set number of sorting and compression threads [1] + memory: + type: string? + inputBinding: + prefix: -m + doc: | + Set maximum memory per thread; suffix K/M/G recognized [768M] + input: + type: File + inputBinding: + position: 1 + + doc: Input bam file. + output_name: + type: string + inputBinding: + position: 2 + + doc: Desired output filename. + sort_by_name: + type: boolean? + inputBinding: + prefix: -n + + doc: Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates. +outputs: + sorted: + type: File + outputBinding: + glob: $(inputs.output_name) + +baseCommand: [samtools, sort] +arguments: +- -f +$namespaces: + s: http://schema.org/ + +$schemas: +- http://schema.org/docs/schema_org_rdfa.html + +s:mainEntity: + $import: samtools-metadata.yaml + +s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-sort.cwl +s:codeRepository: https://github.com/common-workflow-language/workflows +s:license: http://www.apache.org/licenses/LICENSE-2.0 + +s:isPartOf: + class: s:CreativeWork + s:name: Common Workflow Language + s:url: http://commonwl.org/ + +s:author: + class: s:Person + s:name: Andrey Kartashov + s:email: mailto:[email protected] + s:sameAs: + - id: http://orcid.org/0000-0001-9102-5681 + s:worksFor: + - class: s:Organization + s:name: Cincinnati Children's Hospital Medical Center + s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026 + s:department: + - class: s:Organization + s:name: Barski Lab +doc: | + samtools-sort.cwl is developed for CWL consortium + Usage: samtools sort [options...] [in.bam] + Options: + -l INT Set compression level, from 0 (uncompressed) to 9 (best) + -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] + -n Sort by read name + -o FILE Write final output to FILE rather than standard output + -O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or + -T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required) + -@ INT Set number of sorting and compression threads [1] + + Legacy usage: samtools sort [options...] <in.bam> <out.prefix> + Options: + -f Use <out.prefix> as full final filename rather than prefix + -o Write final output to stdout rather than <out.prefix>.bam + -l,m,n,@ Similar to corresponding options above + + diff --git a/debian/samtools-view.cwl b/debian/samtools-view.cwl new file mode 100755 index 0000000..f1b1d94 --- /dev/null +++ b/debian/samtools-view.cwl @@ -0,0 +1,242 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: CommandLineTool + +requirements: +- $import: envvar-global.yml +- $import: samtools-docker.yml +- class: InlineJavascriptRequirement + +inputs: + isbam: + type: boolean + default: false + inputBinding: + position: 2 + prefix: -b + doc: | + output in BAM format + readswithoutbits: + type: int? + inputBinding: + position: 1 + prefix: -F + doc: | + only include reads with none of the bits set in INT set in FLAG [0] + collapsecigar: + type: boolean + default: false + inputBinding: + position: 1 + prefix: -B + doc: | + collapse the backward CIGAR operation + readsingroup: + type: string? + inputBinding: + position: 1 + prefix: -r + doc: | + only include reads in read group STR [null] + bedoverlap: + type: File? + inputBinding: + position: 1 + prefix: -L + doc: | + only include reads overlapping this BED FILE [null] + uncompressed: + type: boolean + default: false + inputBinding: + position: 1 + prefix: -u + doc: | + uncompressed BAM output (implies -b) + readtagtostrip: + type: string[]? + inputBinding: + position: 1 + + doc: | + read tag to strip (repeatable) [null] + input: + type: File + inputBinding: + position: 4 + + doc: | + Input bam file. + readsquality: + type: int? + inputBinding: + position: 1 + prefix: -q + doc: | + only include reads with mapping quality >= INT [0] + readswithbits: + type: int? + inputBinding: + position: 1 + prefix: -f + doc: | + only include reads with all bits set in INT set in FLAG [0] + cigar: + type: int? + inputBinding: + position: 1 + prefix: -m + doc: | + only include reads with number of CIGAR operations + consuming query sequence >= INT [0] + iscram: + type: boolean + default: false + inputBinding: + position: 2 + prefix: -C + doc: | + output in CRAM format + threads: + type: int? + inputBinding: + position: 1 + prefix: -@ + doc: | + number of BAM compression threads [0] + fastcompression: + type: boolean + default: false + inputBinding: + position: 1 + prefix: '-1' + doc: | + use fast BAM compression (implies -b) + samheader: + type: boolean + default: false + inputBinding: + position: 1 + prefix: -h + doc: | + include header in SAM output + count: + type: boolean + default: false + inputBinding: + position: 1 + prefix: -c + doc: | + print only the count of matching records + randomseed: + type: float? + inputBinding: + position: 1 + prefix: -s + doc: | + integer part sets seed of random number generator [0]; + rest sets fraction of templates to subsample [no subsampling] + referencefasta: + type: File? + inputBinding: + position: 1 + prefix: -T + doc: | + reference sequence FASTA FILE [null] + region: + type: string? + inputBinding: + position: 5 + + doc: | + [region ...] + readsingroupfile: + type: File? + inputBinding: + position: 1 + prefix: -R + doc: | + only include reads with read group listed in FILE [null] + readsinlibrary: + type: string? + inputBinding: + position: 1 + prefix: -l + doc: | + only include reads in library STR [null] + output_name: + type: string + inputBinding: + position: 2 + prefix: -o +outputs: + output: + type: File + outputBinding: + glob: $(inputs.output_name) + +baseCommand: [samtools, view] +$namespaces: + s: http://schema.org/ + +$schemas: +- http://schema.org/docs/schema_org_rdfa.html + +s:mainEntity: + $import: samtools-metadata.yaml + +s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-view.cwl +s:codeRepository: https://github.com/common-workflow-language/workflows +s:license: http://www.apache.org/licenses/LICENSE-2.0 + +s:isPartOf: + class: s:CreativeWork + s:name: Common Workflow Language + s:url: http://commonwl.org/ + +s:author: + class: s:Person + s:name: Andrey Kartashov + s:email: mailto:[email protected] + s:sameAs: + - id: http://orcid.org/0000-0001-9102-5681 + s:worksFor: + - class: s:Organization + s:name: Cincinnati Children's Hospital Medical Center + s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026 + s:department: + - class: s:Organization + s:name: Barski Lab +doc: | + samtools-view.cwl is developed for CWL consortium + Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...] + + Options: -b output BAM + -C output CRAM (requires -T) + -1 use fast BAM compression (implies -b) + -u uncompressed BAM output (implies -b) + -h include header in SAM output + -H print SAM header only (no alignments) + -c print only the count of matching records + -o FILE output file name [stdout] + -U FILE output reads not selected by filters to FILE [null] + -t FILE FILE listing reference names and lengths (see long help) [null] + -T FILE reference sequence FASTA FILE [null] + -L FILE only include reads overlapping this BED FILE [null] + -r STR only include reads in read group STR [null] + -R FILE only include reads with read group listed in FILE [null] + -q INT only include reads with mapping quality >= INT [0] + -l STR only include reads in library STR [null] + -m INT only include reads with number of CIGAR operations + consuming query sequence >= INT [0] + -f INT only include reads with all bits set in INT set in FLAG [0] + -F INT only include reads with none of the bits set in INT + set in FLAG [0] + -x STR read tag to strip (repeatable) [null] + -B collapse the backward CIGAR operation + -s FLOAT integer part sets seed of random number generator [0]; + rest sets fraction of templates to subsample [no subsampling] + -@ INT number of BAM compression threads [0] + + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
