jvarkit

Biostar59647

Last commit

SAM/BAM to XML

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar59647  [options] Files

Usage: biostar59647 [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
  * -r, -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit

Keywords

Creation Date

20131112

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar59647.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar59647Test.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 biostar59647 ? 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/biostar59647.jar -r samtools-0.1.18/examples/toy.fa  samtools-0.1.18/examples/toy.bam |\
xmllint --format -

<?xml version="1.0" encoding="UTF-8"?>
<sam ref="/home/lindenb/samtools-0.1.18/examples/toy.bam" bam="/home/lindenb/samtools-0.1.18/examples/toy.fa">
  <!---r /home/lindenb/samtools-0.1.18/examples/toy.fa /home/lindenb/samtools-0.1.18/examples/toy.bam-->
  <read>
    <name>r001</name>
    <sequence>TTAGATAAAGAGGATACTG</sequence>
    <flags READ_PAIRED="true" READ_MAPPED_IN_PROPER_PAIR="true" READ_UNMAPPED="false" MATE_UNMAPPED="false" READ
_REVERSE_STRAND="false" MATE_REVERSE_STRAND="true" FIRST_IN_PAIR="false" SECOND_IN_PAIR="true" NOT_PRIMARY_ALIGN
MENT="false" READ_FAILS_VENDOR_QUALITY_CHECK="false" READ_IS_DUPLICATE="false" SUPPLEMENTARY_ALIGNMENT="false">1
63</flags>
    <qual>30</qual>
    <chrom index="0">ref</chrom>
    <pos>7</pos>
    <cigar>8M4I4M1D3M</cigar>
    <mate-chrom index="0">ref</mate-chrom>
    <mate-pos>37</mate-pos>
    <align>
      <M read-index="1" read-base="T" ref-index="7" ref-base="T"/>
      <M read-index="2" read-base="T" ref-index="8" ref-base="T"/>
      <M read-index="3" read-base="A" ref-index="9" ref-base="A"/>
      <M read-index="4" read-base="G" ref-index="10" ref-base="G"/>
      <M read-index="5" read-base="A" ref-index="11" ref-base="A"/>
      <M read-index="6" read-base="T" ref-index="12" ref-base="T"/>
      <M read-index="7" read-base="A" ref-index="13" ref-base="A"/>
      <M read-index="8" read-base="A" ref-index="14" ref-base="A"/>
      <I read-index="9" read-base="A"/>
      <I read-index="10" read-base="G"/>
      <I read-index="11" read-base="A"/>
      <I read-index="12" read-base="G"/>
      <M read-index="13" read-base="G" ref-index="15" ref-base="G"/>
      <M read-index="14" read-base="A" ref-index="16" ref-base="A"/>
      <M read-index="15" read-base="T" ref-index="17" ref-base="T"/>
      <M read-index="16" read-base="A" ref-index="18" ref-base="A"/>
      <D ref-index="19" ref-base="G"/>
      <M read-index="17" read-base="C" ref-index="20" ref-base="C"/>
      <M read-index="18" read-base="T" ref-index="21" ref-base="T"/>
      <M read-index="19" read-base="G" ref-index="22" ref-base="G"/>
    </align>
  </read>
  <read>
    <name>r002</name>
    <sequence>AAAAGATAAGGGATAAA</sequence>
    <flags READ_PAIRED="false" READ_MAPPED_IN_PROPER_PAIR="false" READ_UNMAPPED="false" MATE_UNMAPPED="false" RE
AD_REVERSE_STRAND="false" MATE_REVERSE_STRAND="false" FIRST_IN_PAIR="false" SECOND_IN_PAIR="false" NOT_PRIMARY_A
LIGNMENT="false" READ_FAILS_VENDOR_QUALITY_CHECK="false" READ_IS_DUPLICATE="false" SUPPLEMENTARY_ALIGNMENT="fals
e">0</flags>
    <qual>30</qual>
    <chrom index="0">ref</chrom>
    <pos>9</pos>
    <cigar>1S2I6M1P1I1P1I4M2I</cigar>
    <align>
      <S read-index="1" read-base="A"/>
      <I read-index="2" read-base="A"/>
      <I read-index="3" read-base="A"/>
      <M read-index="4" read-base="A" ref-index="9" ref-base="A"/>
      <M read-index="5" read-base="G" ref-index="10" ref-base="G"/>
      <M read-index="6" read-base="A" ref-index="11" ref-base="A"/>
      <M read-index="7" read-base="T" ref-index="12" ref-base="T"/>
      <M read-index="8" read-base="A" ref-index="13" ref-base="A"/>
      <M read-index="9" read-base="A" ref-index="14" ref-base="A"/>
      <I read-index="10" read-base="G"/>
      <I read-index="11" read-base="G"/>
      <M read-index="12" read-base="G" ref-index="15" ref-base="G"/>
(...)

Cited in

http://biorxiv.org/content/early/2014/01/21/001834 “Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements”
“Bacterial production and direct functional screening of expanded molecular libraries for discovering inhibitors of protein aggregation” Science Advances 16 Oct 2019: Vol. 5, no. 10, eaax5108 DOI: 10.1126/sciadv.aax5108
Delivoria D.C., Skretas G. (2022) The Discovery of Peptide Macrocycle Rescuers of Pathogenic Protein Misfolding and Aggregation by Integrating SICLOPPS Technology and Ultrahigh-Throughput Screening in Bacteria. In: Coppock M.B., Winton A.J. (eds) Peptide Macrocycles. Methods in Molecular Biology, vol 2371. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1689-5_12

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