jvarkit

TViewCmd

equivalent of samtools tview

Usage

Usage: tview [options] Files
  Options:
    --clip
      Show clip
      Default: false
    --coverage, --depth
      Number of rows for coverage (hide:<=0)
      Default: 10
    --filter
      A filter expression. Reads matching the expression will be filtered-out. 
      Empty String means 'filter out nothing/Accept all'. See https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj 
      for a complete syntax. 'default' is 'mapqlt(1) || Duplicate() || 
      FailsVendorQuality() || NotPrimaryAlignment() || 
      SupplementaryAlignment()' 
      Default: mapqlt(1) || Duplicate() || FailsVendorQuality() || NotPrimaryAlignment() || SupplementaryAlignment()
    --groupby
      Group Reads by. Data partitioning using the SAM Read Group (see 
      https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can 
      be any combination of sample, library....
      Default: sample
      Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --hideBases
      Hide bases
      Default: false
    --hideHomRef
      Hide HOM_REF variations
      Default: false
    --hideNoCall
      Hide NO_CALL variations
      Default: false
    --insert
      Show insertions
      Default: false
    -layout, --layout
      Layout reads
      Default: pileup
      Possible Values: [pileup, name]
    -left, --leftmargin
      left margin width
      Default: 15
    -maxrows, --maxrowss
      maximum number of rows per read group. -1 == all
      Default: -1
    --noconsensus
      Hide Consensus line
      Default: false
    --nodefaultinterval
      if no interval was provided, don't try to create a default one.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --format, --outputformat
      Output format
      Default: tty
      Possible Values: [tty, plain, html]
    --readName
      Show read name
      Default: false
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    -r, --region
      Interval list
      Default: []
    -V, --variant, --variants, --vcf
      Variant file. if filename ends with '.list' it is interpreted as a list 
      of file (one file per line)
    --version
      print version and exit
    -width, --width
      default screen width
      Default: -1

Keywords

• sam
• bam
• visualization
• terminal

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 tview

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/tview/TViewCmd.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/tview/TViewCmdTest.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 tview ? 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

Example

$ java -jar dist/tview.jar -R toy.fa toy.bam --clip  --groupby sample  --insert  --plain

ref:1-61
          POS: 1.......^^..11..^^^^....^^..21........31...^.....41........51
          REF: AGCATGTT**AGATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNN
               
ndefined_sample      TT**AGATAAAGAGGATA**-CTG               cagcgccat       
                      AAAAGATAAGG**GATAAA    NNNNNNtaggc                    
                  NNNNN**AGCTAA                                             
                                    ATA**GCT--------------CTCAGC            
ample CONSENSUS      TTAAAGNTAANGAGGATAAAGCTG      TAGGC  CTCAGCGCCAT
efined_sample 3          ********  ****   **                ****     
                         ********  ****   **                ****     
                         ********  ****   **                ****     
                     ************************      *****  ***********
                     ************************      *****  ***********
                     ************************      *****  ***********
               ******************************************************
               ******************************************************
               ******************************************************
             0 ******************************************************

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