added Tabix format specification
minor clarification to the format spec
spec
use float for QUAL
added ST
sorry. It is SP not ST
update the BCF spec
Change PL/GL order and SP type

* change the order of PL/GL according to the latest VCF spec
* change the type of SP to int32_t
Spec changes due to samtools-0.1.13 (r926:134) release
Change various items

* allow to change the compression level in BAM output
* use compress level 1 in sorting
* association test
* concatenate BAMs
* allow to threshold on max depth in INDEL calling
Adjust LaTeX item labelling to compile on my machine
Dummy annotations reads and CT/PT tags (discussed Oct/Nov 2011)
Merge pull request #1 from peterjc/annotations

Dummy reads for annotations and CT/PT tags
BCFv2 quick reference
code backup
VCF=>BCF, up to QUAL
bcf->vcf, up to INFO
updated the quick reference
clarified quick reference
cleanup