bcftools view: Output CLR,UGT,CGT tags in -m pair/trio calling. In this version, consistency with output genotypes is not being checked.
bcftools view: prevent segfault when running in plain mode, p1 then does not exist
bcftools view: previous fix in kt_fisher_exact (PV4 annotations, fet.c) was wrong. Will this one work better?
constify input parameter to faidx_fetch_seq
Merge pull request #62 from jts/develop

constify input parameter to faidx_fetch_seq
Warn and use correct bin when bin field is wrong

The abort introduced in pull request #43 (8e3b3f2 "Verify old BIN value
of reads during 'samtools index'") is too Draconian, as this field is
in practice used only during indexing -- so the BAM file is mostly fine.

If we're recalculating it here anyway, we might as well use the corrected
value to generate the index and just warn (in a rate-limited way) about
the anomalous records.
Fix bin calculation for unmapped reads

Unmapped reads should have a CIGAR of "*", but sometimes do not e.g. as
occasionally emitted by bwa.  Our bin calculation has been changed to
base the bin on a 1-base region for reads that are either unmapped or
have no cigar, and now agrees with Picard's for these reads.
bam_pileup: Improved read pair overlaps clipping. Disabled for now as more testing is needed.
Merge branch 'develop' of github.com:samtools/samtools into develop
Revert prematurely-committed bam_pileup work

Revert in-progress change 732ae82e9c8fd52ba6688a7c39a322617716483a
("bam_pileup: Improved read pair overlaps clipping. Disabled for now
as more testing is needed.") for now; Petr will recommit it when the
work is complete.