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Description:

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

Homepage:

https://gitlab.com/german.tischler/biobambam2 https://github.com/gt1/biobambam2

License:

GPL-3 MIT

Versions

Metadata

Description

• 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

Maintainers

• Gentoo Biology Project (sci-biology@gentoo.org) - Type: project

Upstream

• Remote IDs:
  • github: gt1/biobambam2

<pkgmetadata>
	<maintainer type="project">
		<email>sci-biology@gentoo.org</email>
		<name>Gentoo Biology Project</name>
	</maintainer>
	<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/biobambam2</remote-id>
	</upstream>
</pkgmetadata>

Lint Warnings

• [Warning] Missing md5-cache for version 9999. Run 'ebuild <ebuild_file> manifest' or 'egencache' to generate it.
• [Warning] Missing md5-cache for version 2.0.146. Run 'ebuild <ebuild_file> manifest' or 'egencache' to generate it.

Manifest