Adding -f flag to samtools sort to give output name directly.
bcftools view: always output the header, even when no other arguments are given
backup commit
Fix memory leaks:
* When downloading a remote FASTA index
* When indexing a BAM, we can't open the FAI file
* When indexing a BCF, we can't open the index file
* Parsing a VCF header with no sample line
* Encountering multiple adjacent tabs in a SAM header
Merge pull request #30 from leecbaker/master

Fixed several small memory leaks.
bcftools view: Exit with an error if the -l file cannot be read
Merge branch 'master' of github.com:samtools/samtools
backup commit
Merge remote branch 'remotes/master/master' into fb-annots
Fixed brackets missing in the previous commit
mpileup: New HWE, QBD, RPS annotations. Modified VDB (beware: this version of VDB may be broken). Fix in indel calling: Ignore insertions with N's. Output contigs in the VCF header. New sam_header2tbl_n() API call.
Updated man pages
Get rid of %ld-with-int64_t warning on Mac
Merge remote branch 'pd3master/master'
Updated NEWS document
Version bump
bcftools: version bump
mpileup fix: Print error message and exit when no files given. (On behalf of Gert Hulselmans)
mpileup indel hotfix: fix in detecting long stretches of N's. The version string can be now overriden, either directly or using git-stamp Makefile rule
The indel stats (IS) annotation splitted into two: IDV and IMF