jvarkit

Biostar172515

Last commit

Convert BAI to XML

Usage

Usage: biostar172515 [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

See also in Biostars

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar172515

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/biostar/Biostar172515.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite biostar172515 ? 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

$ find DIR -name "*.bam" | xargs java -jar dist/biostar172515.jar  | xmllint --format -

<?xml version="1.0" encoding="UTF-8"?>
<bai-list>
<bam bam="DIR/exampleBAM.bam" has-index="true" n_ref="1">
    <reference ref-id="0" ref-name="chr1" ref-length="100000" n_aligned="33" n_bin="12" n_no_coor="0">
      <bin first-locus="1" last-locus="536870912" level="0" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="67108864" level="1" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="8388608" level="2" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="1048576" level="3" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="131072" level="4" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="16384" level="5" first-offset="828" n_chunk="1">
        <chunk chunk_beg="828" chunk_end="1963"/>
      </bin>
      <bin first-locus="16385" last-locus="32768" level="5" first-offset="1963" n_chunk="1">
        <chunk chunk_beg="1963" chunk_end="3323"/>
      </bin>
      <bin first-locus="32769" last-locus="49152" level="5" first-offset="3323" n_chunk="1">
        <chunk chunk_beg="3323" chunk_end="4687"/>
      </bin>
      <bin first-locus="49153" last-locus="65536" level="5" first-offset="4687" n_chunk="1">
        <chunk chunk_beg="4687" chunk_end="6501"/>
      </bin>
      <bin first-locus="65537" last-locus="81920" level="5" first-offset="0" n_chunk="0"/>
      <bin first-locus="81921" last-locus="98304" level="5" first-offset="6501" n_chunk="1">
        <chunk chunk_beg="6501" chunk_end="238223360"/>
      </bin>
      <bin first-locus="98305" last-locus="114688" level="5" first-offset="0" n_chunk="0"/>
    </reference>
  </bam>
  <bam bam="/DIR/exampleBAM2.bam" has-index="true" n_ref="1">
    <reference ref-id="0" ref-name="chr1" ref-length="100000" n_aligned="33" n_bin="12" n_no_coor="0">
      <bin first-locus="1" last-locus="536870912" level="0" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="67108864" level="1" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="8388608" level="2" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="1048576" level="3" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="131072" level="4" first-offset="0" n_chunk="0"/>
      <bin first-locus="1" last-locus="16384" level="5" first-offset="828" n_chunk="1">
        <chunk chunk_beg="828" chunk_end="1963"/>
      </bin>
      <bin first-locus="16385" last-locus="32768" level="5" first-offset="1963" n_chunk="1">
        <chunk chunk_beg="1963" chunk_end="3323"/>
      </bin>
      <bin first-locus="32769" last-locus="49152" level="5" first-offset="3323" n_chunk="1">
        <chunk chunk_beg="3323" chunk_end="4687"/>
      </bin>
      <bin first-locus="49153" last-locus="65536" level="5" first-offset="4687" n_chunk="1">
        <chunk chunk_beg="4687" chunk_end="6501"/>
      </bin>
      <bin first-locus="65537" last-locus="81920" level="5" first-offset="0" n_chunk="0"/>
      <bin first-locus="81921" last-locus="98304" level="5" first-offset="6501" n_chunk="1">
        <chunk chunk_beg="6501" chunk_end="238223360"/>
      </bin>
      <bin first-locus="98305" last-locus="114688" level="5" first-offset="0" n_chunk="0"/>
    </reference>
  </bam>
</bai-list>