Updated JSON

Long overdue update to the interface to JSON, used by ReadFilter.

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:

1. Extensive unit testing
2. Switch to the Apache2 license and removal of all GPLv3 related code
3. Addition of BFC for error correction and FermiAssembler for assemblies
4. Separation of the BLAT capabilities into a separate branch which carries Jim Kent's license
5. Command-line tool (seqtools) for performing rapid assemblies, error correction and re-alignment all in one step
6. 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
7. 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)

v0.3.0

Improved integration with Snowman

v0.2.0

Added support for BamStats

v0.1.6

fixed off by one issue

v0.1.5

Updated the build to optionally handle integration with Boost.