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Bug#854774: ITP: libseqlib -- C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>

* Package name    : libseqlib
  Version         : 1.1.1
  Upstream Author : Jeremiah A. Wala <jwala@broadinstitue.org>
* URL             : https://github.com/walaj/SeqLib
* License         : Apache-2.0
  Programming Lang: C++
  Description     : C++ htslib/bwa-mem/fermi interface for interrogating sequence data
 C++ API and command line tool that provides a rapid and user-friendly
 interface to BAM/SAM/CRAM files, global sequence alignment operations
 and sequence assembly. Four C libraries perform core operations in
 SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment
 and Fermi for error correction and sequence assembly. Benchmarking
 indicates that SeqLib has lower CPU and memory requirements than leading
 C++ sequence analysis APIs. Minimal SeqLib code can extract, error-correct
 and assemble reads from a CRAM file and then align with BWA-MEM.
 SeqLib also provides additional capabilities, including chromosome-aware
 interval queries and read plotting. Command line tools are available for
 performing integrated error correction, micro-assemblies and alignment.

Remark: This library is needed to package freebayes >=1.1.  While freebayes
 1.0 is in new queue currently this package is to enable upgrading it to
 its next version.  When packaging the library some incompatibility between
 libbwa and libfml was detected which was solved by SeqLib upstream with
 patched code copies.  These code copies were removed and the Debian packaged
 libfml was patched instead and uploaded to experimental.  As long as we
 are in freeze it should stay in experimental thus the first upload of
 libseqlib will also be uploaded to experimental.
 The package will be maintained by the Debian Med team at

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