Biostar59647
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
- sam
- bam
- xml
See also in Biostars
Creation Date
20131112
Source code
Unit Tests
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