jvarkit
Bam2Xml
converts a BAM to XML
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar bam2xml [options] Files
Usage: bam2xml [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
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
-R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard/gatk CreateSequenceDictionary or samtools dict
--regions
Limit analysis to this interval. A source of intervals. The following
suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz,
gtf.gz.Otherwise it could be an empty string (no interval) or a list of
plain interval separated by '[ \t\n;,]'
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--validation-stringency
SAM Reader Validation Stringency
Default: LENIENT
Possible Values: [STRICT, LENIENT, SILENT]
--version
print version and exit
Keywords
- sam
- bam
- xml
Creation Date
20130506
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 bam2xml ? 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
samtools view samtools-1.4/examples/toy.sam |\
java -jar dist/bam2xml.jar | xmllint --format -
<?xml version="1.0" encoding="UTF-8"?>
<sam>
<header version="1.5" sort="unsorted">
<dict size="0"/>
<read-groups/>
<program-records/>
</header>
<record id="1" flag="163" length="19" read-paired="true" proper-pair="true" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="true" first-of-pair="false" second-of-pair="true" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref" tid="-1" align-start="7" unclipped-align-start="7" align-end="22" unclipped-align-end="22" mapq="30" mate-ref-name="ref" mate-tid="-1" mate-align-start="37" insert-size="39">
<name>r001</name>
<seq>TTAGATAAAGAGGATACTG</seq>
<cigar>
<ce op="M" length="8" read-pos="0" ref-pos="7"/>
<ce op="I" length="4" read-pos="8"/>
<ce op="M" length="4" read-pos="12" ref-pos="15"/>
<ce op="D" length="1" ref-pos="19"/>
<ce op="M" length="3" read-pos="16" ref-pos="20"/>
</cigar>
<attributes>
<attribute name="XX">[S@1e81f4dc</attribute>
</attributes>
</record>
<record id="2" flag="0" length="17" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref" tid="-1" align-start="9" unclipped-align-start="8" align-end="18" unclipped-align-end="18" mapq="30">
<name>r002</name>
<seq>AAAAGATAAGGGATAAA</seq>
<cigar>
<ce op="S" length="1" read-pos="0" ref-pos="8"/>
<ce op="I" length="2" read-pos="1"/>
<ce op="M" length="6" read-pos="3" ref-pos="9"/>
<ce op="P" length="1"/>
<ce op="I" length="1" read-pos="9"/>
<ce op="P" length="1"/>
<ce op="I" length="1" read-pos="10"/>
<ce op="M" length="4" read-pos="11" ref-pos="15"/>
<ce op="I" length="2" read-pos="15"/>
</cigar>
<attributes/>
</record>
<record id="3" flag="0" length="6" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref" tid="-1" align-start="9" unclipped-align-start="4" align-end="14" unclipped-align-end="14" mapq="30">
<name>r003</name>
<seq>AGCTAA</seq>
<cigar>
<ce op="H" length="5" ref-pos="4"/>
<ce op="M" length="6" read-pos="0" ref-pos="9"/>
</cigar>
<attributes/>
</record>
<record id="4" flag="0" length="12" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref" tid="-1" align-start="16" unclipped-align-start="16" align-end="40" unclipped-align-end="40" mapq="30">
<name>r004</name>
<seq>ATAGCTCTCAGC</seq>
<cigar>
<ce op="M" length="6" read-pos="0" ref-pos="16"/>
<ce op="N" length="14" ref-pos="22"/>
<ce op="I" length="1" read-pos="6"/>
<ce op="M" length="5" read-pos="7" ref-pos="36"/>
</cigar>
<attributes/>
</record>
<record id="5" flag="16" length="5" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="true" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref" tid="-1" align-start="29" unclipped-align-start="23" align-end="33" unclipped-align-end="33" mapq="30">
<name>r003</name>
<seq>TAGGC</seq>
<cigar>
<ce op="H" length="6" ref-pos="23"/>
<ce op="M" length="5" read-pos="0" ref-pos="29"/>
</cigar>
<attributes/>
</record>
<record id="6" flag="83" length="9" read-paired="true" proper-pair="true" read-unmapped="false" mate-unmapped="false" read-reverse-strand="true" mate-reverse-strand="false" first-of-pair="true" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref" tid="-1" align-start="37" unclipped-align-start="37" align-end="45" unclipped-align-end="45" mapq="30" mate-ref-name="ref" mate-tid="-1" mate-align-start="7" insert-size="-39">
<name>r001</name>
<seq>CAGCGCCAT</seq>
<cigar>
<ce op="M" length="9" read-pos="0" ref-pos="37"/>
</cigar>
<attributes/>
</record>
<record id="7" flag="0" length="20" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref2" tid="-1" align-start="1" unclipped-align-start="1" align-end="20" unclipped-align-end="20" mapq="30">
<name>x1</name>
<seq>AGGTTTTATAAAACAAATAA</seq>
<qual>????????????????????</qual>
<cigar>
<ce op="M" length="20" read-pos="0" ref-pos="1"/>
</cigar>
<attributes/>
</record>
<record id="8" flag="0" length="21" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref2" tid="-1" align-start="2" unclipped-align-start="2" align-end="22" unclipped-align-end="22" mapq="30">
<name>x2</name>
<seq>GGTTTTATAAAACAAATAATT</seq>
<qual>?????????????????????</qual>
<cigar>
<ce op="M" length="21" read-pos="0" ref-pos="2"/>
</cigar>
<attributes/>
</record>
<record id="9" flag="0" length="26" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref2" tid="-1" align-start="6" unclipped-align-start="6" align-end="27" unclipped-align-end="27" mapq="30">
<name>x3</name>
<seq>TTATAAAACAAATAATTAAGTCTACA</seq>
<qual>??????????????????????????</qual>
<cigar>
<ce op="M" length="9" read-pos="0" ref-pos="6"/>
<ce op="I" length="4" read-pos="9"/>
<ce op="M" length="13" read-pos="13" ref-pos="15"/>
</cigar>
<attributes/>
</record>
<record id="10" flag="0" length="25" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref2" tid="-1" align-start="10" unclipped-align-start="10" align-end="34" unclipped-align-end="34" mapq="30">
<name>x4</name>
<seq>CAAATAATTAAGTCTACAGAGCAAC</seq>
<qual>?????????????????????????</qual>
<cigar>
<ce op="M" length="25" read-pos="0" ref-pos="10"/>
</cigar>
<attributes/>
</record>
<record id="11" flag="0" length="24" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref2" tid="-1" align-start="12" unclipped-align-start="12" align-end="35" unclipped-align-end="35" mapq="30">
<name>x5</name>
<seq>AATAATTAAGTCTACAGAGCAACT</seq>
<qual>????????????????????????</qual>
<cigar>
<ce op="M" length="24" read-pos="0" ref-pos="12"/>
</cigar>
<attributes/>
</record>
<record id="12" flag="0" length="23" read-paired="false" proper-pair="false" read-unmapped="false" mate-unmapped="false" read-reverse-strand="false" mate-reverse-strand="false" first-of-pair="false" second-of-pair="false" not-primary-alignment="false" read-fails-vendor-quality-check="false" duplicate-read="false" supplementary-alignment="false" ref-name="ref2" tid="-1" align-start="14" unclipped-align-start="14" align-end="36" unclipped-align-end="36" mapq="30">
<name>x6</name>
<seq>TAATTAAGTCTACAGAGCAACTA</seq>
<qual>???????????????????????</qual>
<cigar>
<ce op="M" length="23" read-pos="0" ref-pos="14"/>
</cigar>
<attributes/>
</record>
</sam>