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?
Include htslib in our build directory

Eventually perhaps we'll be able to install an htslib-dev package
during before_install instead.
Include htslib rules and add header dependencies

Use the rules and variables from htslib.mk to write out exact
dependencies on htslib headers and (for executables) library.
With this, samtools builds with "make" from here are correct
even when htslib source code is being modified.

(A little more infrastructure is needed to select between static
and shared libhts.)
Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
Added a test suite for samtools, currently faidx and bgzip are tested.
Added a test suite for samtools, currently faidx and bgzip are tested.
tview and bgzip: Check that the files are bgzipped, not gzipped.
constify input parameter to faidx_fetch_seq
Fix buglet: initialise the kstring_t

Also parse "" rather than NULL in the unlikely event of an empty .fai
file, and add a bam_import.o prerequisite that was omitted.
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.)
This is a backup commit. Samtools mpileup seems to be working well in this version, but should be still considered experimental.