Biostar172515

##Motivation

Convert BAI to XML (see https://www.biostars.org/p/172515/)

##Compilation

See also Compilation.

$  make biostar172515

##Synopsis

$ java -jar dist/biostar172515.jar  *.bam

Options

• -o,--output output file.
• -h,--help print help
• -version,--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar172515.java

See also

https://www.biostars.org/p/172515/https://www.biostars.org/p/172515/

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 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>

Contribute

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

##History

• 2016 : Creation

License

The project is licensed under the MIT license.