Package: wnpp Severity: wishlist Owner: Andreas Tille <ti...@debian.org>
* Package name : libseqlib Version : 1.1.1 Upstream Author : Jeremiah A. Wala <jw...@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 https://anonscm.debian.org/git/debian-med/libseqlib.git
