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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription lang="en">
This package contains some tools for processing BAM files including
bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
bamsort: reads BAM and writes BAM resorted by coordinates or query name
bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
</longdescription>
<upstream>
<remote-id type="github">gt1/biobambam</remote-id>
</upstream>
</pkgmetadata>
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