Releases: walaj/SeqLib
Updated JSON
Minor release: Improved tag handling
-- Improved tag handling, which now returns false if tag not present. This allows for the distinction between tag with value 0 and non-existent tags.
-- Added GetFloatTag
-- Bug fixes to edge cases in Qualities
-- Simpler implementation of BFC
Release to sync with Broad installation
Minor release which addresses an issue where white-spaces were not accepted as delimiters for BED files. This release is mainly to sync with BITS installation of Snowman SV detection on Broad servers.
Remote BAM support, etc
-- Support (via htslib) for remote BAM access for FTP, HTTPS, Google Cloud etc.
-- Additional parameters for FermiAssembler are now accessible
-- Improved FASTQ/FASTA reading are now incorporated into FastqReader (via klib).
Minor issues resolved:
-- name collision when linking both fermi and bwa
-- zlib now used for reading gzipped VCF and BED files in GenomicRegionCollection
-- more GenomicRegionCollection interval ops are templated in both the query and subject
-- fixed issue where kt_for was unnecessarily spawning new threads in BFC
Bug fixes to multi bam reading and cigar setting
- Added HeaderConcat to retrieve multiple headers from a multi-bam reader
- Fixed bug in SetCigar
- Fixed bug in GetNextRecord for multiple bams
The binaries are for the Apache2 branch (master).
Initial release of newly redesigned "SeqLib"
This is a more mature release of the old "SnowTools", under a new name and after a massive overhaul. This SeqLib release contains the following new additions:
- Extensive unit testing
- Switch to the Apache2 license and removal of all GPLv3 related code
- Addition of BFC for error correction and FermiAssembler for assemblies
- Separation of the BLAT capabilities into a separate branch which carries Jim Kent's license
- Command-line tool (seqtools) for performing rapid assemblies, error correction and re-alignment all in one step
- Unravels a lot of the functionality into separate pieces (e.g. BamReader and BamWriter now separate entities), which makes for more understandable and versatile code
- Removal of all dependencies on Boost
SeqLib is also now integrated into VariantBam (https://github.com/jwalabroad/VariantBam) and SnowmanSV (https://github.com/broadinstitute/SnowmanSV)