jvarkit

CoverageServer

Jetty Based http server serving Bam coverage.

Usage

Usage: java -jar dist/coverageserver.jar  [options] Files
Usage: coverageserver [options] Files
  Options:
    --bed, --B
      Optional bed file containing user's intervals. 4th column is used as the 
      name of the interval
    -o, --output, --comment
      Output file for writing comments as a BED file. Very basic= not suitable 
      for multiple users.
    --extend
      Extend interval by this factor. e.g: if x='0.5' chr1:100-200 -> 
      chr1:50-250 
      Default: 1.0
    --gtf
      Optional Tabix indexed GTF file. Will be used to retrieve an interval by 
      gene name, or to display gene names in a region.
    --height
      Image height
      Default: 300
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --link, --url, --hyperlink
      creates a hyperlink when 'click' in an area. The URL must contains 
      __CHROM__, __START__ and __END__ that will be replaced by their values. 
      Predefined values are 'hg19','hg38','igv'. IGV : 
      "http://localhost:60151/goto?locus=__CHROM__%3A__START__-__END__" , 
      UCSC: "http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg19&position=__CHROM__%3A__START__-__END__"
      Default: <empty string>
    --images-per-row, --ipr
      Number of images per row.
      Default: 2
    --vcf, --region, --regions, --intervals
      Same as --bed but intervals won't be annotated. A source of intervals. 
      The following suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, 
      gff, gff.gz, gtf.gz.Otherwise it could be an empty string (no interval) 
      or a list of plain interval separated by '[ \t\n;,]'
      Default: (empty)
    --known
      Optional Tabix indexed Bed or VCF file containing known CNV. Both types 
      must be indexed.
    --mapq
      Min. Read Mapping Quality.
      Default: 0
    --max_-size
      Security for memory. Max interval size. A distance specified as a 
      positive integer.Commas are removed. The following suffixes are 
      interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 10000000
    --pedigree, -p
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0|.|undefined|unknown:unknown;1|male|M:male;2|female|F:female), 
      phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    --port
      server port.
      Default: 8080
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --sashimi
      Enable sashimi plots.
      Default: false
    --small-length
      show reads if the region has a length <= 'x'.
      Default: 1000
    --version
      print version and exit
    --width
      Image width
      Default: 500

Keywords

• cnv
• bam
• coverage
• server

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew coverageserver

The java jar file will be installed in the dist directory.

Creation Date

20200212

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/coverageserver/CoverageServer.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite coverageserver ? 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

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

input

input is a set of indexed BAM file or a file with the suffix .list containing the path to the bams.

Example

java -jar dist/jvarkit.jar coverageserver \
	--pedigree fam.ped \
	--bed roi.bed \
	-o comments.bed \
	-R ref.fasta src/test/resources/S*.bam

Hidden http parameters

• columns=5 change the number of columns at runtime.

Screenshot

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