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.
Set samtools sort's exit status from errors

If bam_merge_core2() fails, this needs to be reflected in the exit status.
Fix samtools sort -f temporary file names

Pull request #27 introduced a bug in which worker threads wrote
temporary files with different names (prefix.NNNN.bam) to those the
merge step tried to read (prefix.NNNN).

Now bam_sort_core_ext() has separate prefix and output filename
parameters, enabling future code allowing the temporary files to be
somewhere entirely separate from the output file (e.g., $TMPDIR).

(With -f, temporary files now have slightly odd names such as
foo.bam.0001.bam, but they're only temporary anyway...
Thanks to Chris Carr for reporting this bug.)
Merge branch 'with-htslib' into develop

The mainline development samtools now requires the separate htslib library.
Remove recursive make for "misc" subdirectory

This was the last remaining vestige of the "all-recur" recursive build.

Also remove the embryonic shared library rules for libbam.so.1 and
libbam.1.dylib, which never fully versioned the shared objects.
Tidy up makefile

Add the conventional $(CPPFLAGS) and $(LDFLAGS).

Remove the htslib-specific parts of the version number calculations,
and put the comments back.

Also add a "tags" target.
Fix typo, remove razip vestige [minor]
stats: Removed unused stats code (NMQ)
mpileup: Updated to the latest htslib API; disabled tie correction in MWU for now, as the results look suspicious
mpileup: Updated to htslib vcf module changes
Resolved merge conflicts