compiling error
optionally output OQ instead of QUAL
Merge branch 'lite'

Conflicts:
	bam2fq.c
correct typos
deal with Number=A and Number=G INFO and FORMAT fields when trimming alleles
add new tool vcfsubset
add tests for vcfsubset
resolved test/check.chk conflict
vcfsubset: New -i,-e options for general filter expressions. In this version, only QUAL and INFO columns are supported.
vcffilter: Change in neighbourhood function in SOM training, seems more robust with respect to random seed
Merge branch 'master' into develop

Note that we aim to check new work into the develop branch; nothing
should go directly to master.  This merges past changes accidentally
committed to master.
vcf core lib, vcfsubset, vcfmerge: First step towards binary BCF output. Functional but probably buggy.
Resolved vcfmerge.c merge conflict
vcfsubset: Make --apply-filters consistent with other tools
Merge remote branch 'remotes/sm15-mod/develop' into develop
Move format specifications to sam-spec repository

These documents (along with their history) have been moved
to https://github.com/samtools/sam-spec
Test with both Clang and GCC
vcfcheck: re-enabled stats by QUAL
Merge branch 'develop' of github.com:samtools/htslib into develop
Deleted files which were moved to the new samtools/bcftools.git repository