From 6fe7338c21ccfa9d901656d581c3e183d65a3a46 Mon Sep 17 00:00:00 2001 From: lindenb Date: Thu, 18 Apr 2024 09:55:14 +0200 Subject: [PATCH] fix doc --- build.gradle | 2 +- docs/AddLinearIndexToBed.md | 4 +- docs/BamLiftOver.md | 4 +- docs/BedCluster.md | 4 +- docs/BedRemoveBed.md | 4 +- docs/BigwigMerge.md | 103 ++++++++++++++++++ docs/ConvertBamChromosomes.md | 6 +- docs/IbdToVcf.md | 4 +- docs/JvarkitCentral.md | 4 +- docs/SwingIndexCov.md | 4 +- docs/VcfFilterByLiftOver.md | 95 ++++++++++++++++ docs/index.md | 5 +- mkdocs.yml | 1 + .../tools/bigwigmerge/BigwigMerge.java | 10 +- 14 files changed, 225 insertions(+), 25 deletions(-) create mode 100644 docs/BigwigMerge.md create mode 100644 docs/VcfFilterByLiftOver.md diff --git a/build.gradle b/build.gradle index 2efab6f93..fc08a0ac4 100644 --- a/build.gradle +++ b/build.gradle @@ -1286,7 +1286,7 @@ all2.add( task("svneg", type: CompileJVarkit) { jarLibs = combineLibs("htsjdk","testng","jcommander") }); all.add( task("sigframe", type: CompileJVarkit) { - mainClass = "com.github.lindenb.jvarkit.tools.sigframe.SigFrame" + mainClass = "com.github.lindenb.jvarkit.tools.sigframe.SigFrame.Main" jarLibs = combineLibs("htsjdk","testng","jcommander") }); all.add( task("simpleplot", type: CompileJVarkit) { diff --git a/docs/AddLinearIndexToBed.md b/docs/AddLinearIndexToBed.md index 676661dcc..eb2a7ca79 100644 --- a/docs/AddLinearIndexToBed.md +++ b/docs/AddLinearIndexToBed.md @@ -24,8 +24,8 @@ Usage: addlinearindextobed [options] Files Output file. Optional . Default: stdout * -R, --reference, --dict A SAM Sequence dictionary source: it can be a *.dict file, a fasta file - indexed with 'picard CreateSequenceDictionary', or any hts file - containing a dictionary (VCF, BAM, CRAM, intervals...) + indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or + any hts file containing a dictionary (VCF, BAM, CRAM, intervals...) --version print version and exit diff --git a/docs/BamLiftOver.md b/docs/BamLiftOver.md index 62e133581..95ba6afdd 100644 --- a/docs/BamLiftOver.md +++ b/docs/BamLiftOver.md @@ -23,8 +23,8 @@ Usage: bamliftover [options] Files LiftOver file. * -R2, --destination-dict A SAM Sequence dictionary source: it can be a *.dict file, a fasta file - indexed with 'picard CreateSequenceDictionary', or any hts file - containing a dictionary (VCF, BAM, CRAM, intervals...) + indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or + any hts file containing a dictionary (VCF, BAM, CRAM, intervals...) --drop-seq drop SEQ and QUAL Default: false diff --git a/docs/BedCluster.md b/docs/BedCluster.md index 60078cd14..e8d218245 100644 --- a/docs/BedCluster.md +++ b/docs/BedCluster.md @@ -51,8 +51,8 @@ Usage: bedcluster [options] Files -R, --reference For sorting, writing interval_list,A SAM Sequence dictionary source: it can be a *.dict file, a fasta file indexed with 'picard - CreateSequenceDictionary', or any hts file containing a dictionary (VCF, - BAM, CRAM, intervals...) + CreateSequenceDictionary' or 'samtools dict', or any hts file containing + a dictionary (VCF, BAM, CRAM, intervals...) --sex, --par Detects human dictionary ans splits pseudo-autosomal regions and group by sex. diff --git a/docs/BedRemoveBed.md b/docs/BedRemoveBed.md index d521b43e6..577a4a302 100644 --- a/docs/BedRemoveBed.md +++ b/docs/BedRemoveBed.md @@ -28,8 +28,8 @@ Usage: bedremovebed [options] Files Output is a setfile. Output file. Optional . Default: stdout -R, -r, --reference A SAM Sequence dictionary source: it can be a *.dict file, a fasta file - indexed with 'picard CreateSequenceDictionary', or any hts file - containing a dictionary (VCF, BAM, CRAM, intervals...) + indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or + any hts file containing a dictionary (VCF, BAM, CRAM, intervals...) --version print version and exit diff --git a/docs/BigwigMerge.md b/docs/BigwigMerge.md new file mode 100644 index 000000000..282b0099b --- /dev/null +++ b/docs/BigwigMerge.md @@ -0,0 +1,103 @@ +# BigwigMerge + +![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png) + +merge several Bigwig files using different descriptive statistics (mean, median, etc..) + + +## Usage + + +This program is now part of the main `jvarkit` tool. See [jvarkit](JvarkitCentral.md) for compiling. + + +``` +Usage: java -jar dist/jvarkit.jar bigwigmerge [options] Files + +Usage: bigwigmerge [options] Files + Options: + --header + write track header + Default: false + -h, --help + print help and exit + --helpFormat + What kind of help. One of [usage,markdown,xml]. + --interval, -r + process only this interval + --method, -m + how to compute merge of wiggle values ? + Default: median + Possible Values: [median, average, count, sum, min, max, random] + --min-item-count + skip output data if thre is less than 'x' bigwig file at a location + Default: 0 + --min-value + skip output data with values lower than 'x' + -o, --output + Output file. Optional . Default: stdout + * -R, --reference + A SAM Sequence dictionary source: it can be a *.dict file, a fasta file + indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or + any hts file containing a dictionary (VCF, BAM, CRAM, intervals...) + --version + print version and exit + +``` + + +## Keywords + + * wig + * bigwig + + + +## Creation Date + +20240417 + +## Source code + +[https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java) + + +## Contribute + +- Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues) +- Source Code: [http://github.com/lindenb/jvarkit](http://github.com/lindenb/jvarkit) + +## License + +The project is licensed under the MIT license. + +## Citing + +Should you cite **bigwigmerge** ? [https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md](https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md) + +The current reference is: + +[http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030) + +> Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. +> [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030) + + +# motivation + +merge several Bigwig files using different descriptive statistics (mean, median, etc..) + +Output is a BedGraph file. + +Input is a set of bigwig file or a file with the '.list' suffix containing the path to the bigwig + + +## Example + +``` +find DIR -type f -name "*.bigWig" > tmp.list +java -jar jvarkit.jar bigwigmerge -R genome.fa tmp.list --interval "chr1:234-567" --header --method median > bedGraph.bed +``` + + + diff --git a/docs/ConvertBamChromosomes.md b/docs/ConvertBamChromosomes.md index 35fcf0c2c..bc024dc9b 100644 --- a/docs/ConvertBamChromosomes.md +++ b/docs/ConvertBamChromosomes.md @@ -21,9 +21,9 @@ Usage: bamrenamechr [options] Files Default: 5 --dict Use this new dictionary A SAM Sequence dictionary source: it can be a - *.dict file, a fasta file indexed with 'picard - CreateSequenceDictionary', or any hts file containing a dictionary (VCF, - BAM, CRAM, intervals...) + *.dict file, a fasta file indexed with 'picard CreateSequenceDictionary' + or 'samtools dict', or any hts file containing a dictionary (VCF, BAM, + CRAM, intervals...) -h, --help print help and exit --helpFormat diff --git a/docs/IbdToVcf.md b/docs/IbdToVcf.md index 2fafbffb3..ebbf35689 100644 --- a/docs/IbdToVcf.md +++ b/docs/IbdToVcf.md @@ -34,8 +34,8 @@ Usage: ibd2vcf [options] Files Pedigree file. family-id(space)sample-id. * -R, --reference, --dict A SAM Sequence dictionary source: it can be a *.dict file, a fasta file - indexed with 'picard CreateSequenceDictionary', or any hts file - containing a dictionary (VCF, BAM, CRAM, intervals...) + indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or + any hts file containing a dictionary (VCF, BAM, CRAM, intervals...) --tmpDir tmp working directory. Default: java.io.tmpDir Default: [] diff --git a/docs/JvarkitCentral.md b/docs/JvarkitCentral.md index 16b3df639..5434e39f6 100644 --- a/docs/JvarkitCentral.md +++ b/docs/JvarkitCentral.md @@ -2,8 +2,8 @@ JVARKIT ======= Author : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France. -Version : 9b5c192ab -Compilation : 20240412112112 +Version : 4f4bf4d7d +Compilation : 20240418092015 Github : https://github.com/lindenb/jvarkit Issues : https://github.com/lindenb/jvarkit/issues diff --git a/docs/SwingIndexCov.md b/docs/SwingIndexCov.md index c34aad253..b2b41f8b7 100644 --- a/docs/SwingIndexCov.md +++ b/docs/SwingIndexCov.md @@ -27,8 +27,8 @@ Usage: swingindexcov [options] Files "path/to/helper.jar package.helper.implementation.Name" -R, --reference A SAM Sequence dictionary source: it can be a *.dict file, a fasta file - indexed with 'picard CreateSequenceDictionary', or any hts file - containing a dictionary (VCF, BAM, CRAM, intervals...) + indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or + any hts file containing a dictionary (VCF, BAM, CRAM, intervals...) --version print version and exit diff --git a/docs/VcfFilterByLiftOver.md b/docs/VcfFilterByLiftOver.md new file mode 100644 index 000000000..9b5a5ac4e --- /dev/null +++ b/docs/VcfFilterByLiftOver.md @@ -0,0 +1,95 @@ +# VcfFilterByLiftOver + +![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png) + +Add FILTER(s) to a variant when it is known to map elsewhere after liftover. + + +## Usage + + +This program is now part of the main `jvarkit` tool. See [jvarkit](JvarkitCentral.md) for compiling. + + +``` +Usage: java -jar dist/jvarkit.jar vcffilterbyliftover [options] Files + +Usage: vcffilterbyliftover [options] Files + Options: + --bcf-output + If this program writes a VCF to a file, The format is first guessed from + the file suffix. Otherwise, force BCF output. The current supported BCF + version is : 2.1 which is not compatible with bcftools/htslib (last + checked 2019-11-15) + Default: false + * -f, --chain + LiftOver file. + --generate-vcf-md5 + Generate MD5 checksum for VCF output. + Default: false + -h, --help + print help and exit + --helpFormat + What kind of help. One of [usage,markdown,xml]. + --lifted-filtered-vcf + Another VCF in the destination reference. Input VCF will be filtered if + this vcf is FILTERed at the same lifted position. + -m, --minmatch + lift over min-match. + Default: 1.0 + --no-validation + Disable dictionary validation + Default: false + -o, --out + Output file. Optional . Default: stdout + --version + print version and exit + -D + final distance. We look for weird distance between the current and the + previous variant on the same contig.Two variants initially distance < d + should have a distance Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. +> [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030) + + diff --git a/docs/index.md b/docs/index.md index 18e016530..6d2f4097c 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,8 +2,8 @@ JVARKIT ======= Author : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France. -Version : 9b5c192ab -Compilation : 20240412112112 +Version : 4f4bf4d7d +Compilation : 20240418092015 Github : https://github.com/lindenb/jvarkit Issues : https://github.com/lindenb/jvarkit/issues @@ -158,6 +158,7 @@ Please, read [how to run and install jvarkit](JvarkitCentral.md) | [bamliftover](BamLiftOver.md) | Lift-over a BAM file. | | | | [barcodegenerator](BarcodeGenerator.md) | Barcode generator for EricCharp | 20230629 | 20230629 | | [bedremovebed](BedRemoveBed.md) | Remove bed file from each record of input bed file. Output is a SETFILE | 20221210 | 20221210 | +| [bigwigmerge](BigwigMerge.md) | merge several Bigwig files using different descriptive statistics (mean, median, etc..) | 20240417 | 20240417 | | [bio2rdf](BioToRDF.md) | Build a RDF database for human from misc sources | 20220427 | 20220510 | | [cnvvalidatorserver](CNVValidatorServer.md) | Review files generated by coverageplotter | 20220818 | 20220826 | | [convertliftoverchain](ConvertLiftOverChain.md) | Convert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc...) | 20190409 | 20190409 | diff --git a/mkdocs.yml b/mkdocs.yml index c0089757c..dbaf63eb5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -35,6 +35,7 @@ nav: - "bednonoverlappingset" : BedNonOverlappingSet.md - "bedremovebed" : BedRemoveBed.md - "bedrenamechr" : ConvertBedChromosomes.md + - "bigwigmerge" : BigwigMerge.md - "bio2rdf" : BioToRDF.md - "bioalcidaejdk" : BioAlcidaeJdk.md - "biostar103303" : Biostar103303.md diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java b/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java index f7153e389..ca5f4caf6 100644 --- a/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java +++ b/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java @@ -34,20 +34,20 @@ merge several Bigwig files using different descriptive statistics (mean, median, etc..) Output is a BedGraph file. - -input is a set of bigwig file or a file with the '.list' suffix containing the path to the bigwig - + +Input is a set of bigwig file or a file with the '.list' suffix containing the path to the bigwig + ## Example ``` find DIR -type f -name "*.bigWig" > tmp.list -java -jar ~/jeter8.jar -R genome.fa tmp.list --interval "chr1:234-567" --header > bedGraph.bed +java -jar jvarkit.jar bigwigmerge -R genome.fa tmp.list --interval "chr1:234-567" --header --method median > bedGraph.bed ``` END_DOC - + **/ @Program( name="bigwigmerge",