Previously this info had only been present in the help text emitted from
`bwa mem` without arguments, but I think it helpful to include in man page.

Correct header formatting, fix some typos in headers

The u_int32_t type comes from <sys/types.h>, which is often included
as a byproduct of other headers on glibc platforms, but not on FreeBSD
or Alpine Linux.  Use <stdint.h>'s uint32_t instead, which is used
elsewhere in bwa source code.

Fixes compilation on non-glibc platforms, e.g., FreeBSD and Alpine Linux.

simple URL update for grch38
fixes #111, #115
grch37 link is still valid

Similarly to the realloc(pac,...) within add1(), only bother to call
realloc() if appending the reverse complemented sequence requires more
space than is currently in the pac/m_pac buffer.

Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c"
message from wrap_realloc()) in the corner case of an empty reference
FASTA file.  Fixes #54.

[Based on PR #37 with the additions below.]

Don't free non-malloced items in BWTFree().  If BWTCreate() is ever
called with a non-NULL decodeTable, BWTFree() will need to not free
decodeTable -- see FIXME comment.

Close packedFile in BWTIncConstructFromPacked() in the normal case.
Ignore it in error cases, as they immediately call exit() anyway.

samtools sort v0.7.15+ requires -o flag to specify the output file

In the bwa.c and bwase.c calls, rlen is an int64_t returned from
bns_get_seq() and is the number of reference bases covered by the
alignment; l_query/len is an int and the query length of the alignment;
and the result is an int given to an int parameter of ksw_global[2]().

As even the result is int and as rlen is effectively bounded by the
maximum length of a reference sequence, we maintain the status quo in
this code and simply cast rlen to int to silence Clang's "use llabs()"
(llabs() would not be a great answer given an int64_t anyway).

The bwtsw2_pair.c call needs to remain fabs() so both divisions are
done in floating point; cast to double to prevent Clang suggesting
changing the call to integer abs().

As -o is still free in the mem command, use that standard option to
specify an output file (and keep -f to parallel bwase/bwape commands).
Document it in the usage and man page.

Correct header formatting, fix some typos in headers

This counter is only used in a log message.  Fixes #131.

FASTQ files containing NULs are invalid but should not cause bwa to
crash, as it does if the quality line contains a NUL.  Fixes #122.

Just as we set r.failed and return early if there are no high-quality
read pairs at all, also do so if there are none within the calculated
boundaries.  This avoids returning avg=NAN std=NAN, which leads to
malloc(INFINITY) and a crash; fixes #108.

[Andreas Tille]
Check exact number of arguments of bwtupdate
Fix spelling

[Fabian Klötzl]
change printing as size_t is unsigned

Fail to infer insert size distribution when no pairs are within boundaries (re issue 108)

updates grch38 URL

Add -M option to run-bwamem

Update README.md

Various collected fixes (updated versions of several existing PRs)

BWTFree() is not for build. Only BWTIncFree() is needed.

Forbid literal TAB control characters in @rg line

Typos, doc improvements in man page

Mem should set the mate cigar tag.

Fix output file parameter for samtools sort