jvarkit

BamQueryReadNames

Query a Bam file indexed with BamIndexReadNames

Usage

Usage:  [options] Files
  Options:
    --bamcompression
      Compression Level.
      Default: 5
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit
    -N
       save unmatched names here
    -s
      user list of read names is sorted
      Default: false

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 

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/bamindexnames/BamQueryReadNames.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 ** ? 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

$cat read.names
HWI-1KL149:18:C0RNBACXX:1:1101:12800:7069
HWI-1KL149:18:C0RNBACXX:1:1101:15533:71685
HWI-1KL149:18:C0RNBACXX:1:1103:6001:91243
HWI-1KL149:18:C0RNBACXX:1:1107:2088:3461
HWI-1KL149:18:C0RNBACXX:1:1108:2098:26795
HWI-1KL149:18:C0RNBACXX:1:1110:10318:73043
HWI-1KL149:18:C0RNBACXX:1:1112:18688:6422
HWI-1KL149:18:C0RNBACXX:1:1116:8824:38450/1
HWI-1KL149:18:C0RNBACXX:1:1202:13982:33444/2
ZZZZ:X



$ java -jar dist/bamqueryreadnames.jar -b -s -N list.notfound input.bam read.names | samtools view |head

HWI-1KL149:18:C0RNBACXX:1:1101:12800:7069	77	*	0	0	*	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	##################################################	RG:Z:p1294	AS:i:0	XS:i:0
HWI-1KL149:18:C0RNBACXX:1:1101:12800:7069	141	*	0	0	*	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	##################################################	RG:Z:p1294	AS:i:0	XS:i:0
HWI-1KL149:18:C0RNBACXX:1:1101:15533:71685	99	X	238583	60	100M	=	23858972	274	(...)
(...)

$ cat list.notfound
ZZZZ:X

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