merge r199 changes; part 1
merge r199 changes; part 2
merge r199 changes; part 3
added bam2bed
r198: tag version
r199: reduce one conflict when merged with master
r200: the previous is not good enough
Exported some routines
Allow to skip errors
Append new header lines
do not round per-sample average depths to integer values
Merge pull request #8 from sm15/develop

do not round per-sample average depths to integer values
Synced VCF/BCF reader and most of the vcf*tools now read from stdin. Speedup in
vcf_parse1 by skipping fields which are not needed.
Merge branch 'master' of github.com:samtools/htslib
Updated test file for vcfcheck
vcfnorm fix: segfault on nasty case of indel; synced_reader fix: read from stdin
vcfnorm: Sanity check for reference sequence mismatches
added this missing file
Merge branch 'lite'

Conflicts:
	Makefile
	htslib/hts.h
	htslib/tbx.c
	htslib/vcf.c
	htslib/vcf.h
	main.c
bam2fq: skip secondary alignments