Log Message:
htslib: updated to 1.9

1.9:
If ./configure fails, make will stop working until either configure is re-run \ 
successfully, or make distclean is used. This makes configuration failures more \ 
obvious.

The default SAM version has been changed to 1.6. This is in line with the latest \ 
version specification and indicates that HTSlib supports the CG tag used to \ 
store long CIGAR data in BAM format.

bgzip integrity check option '--test'

Faidx can now index fastq files as well as fasta. The fastq index adds an extra \ 
column to the .fai index which gives the offset to the quality values. New \ 
interfaces have been added to htslib/faidx.h to read the fastq index and \ 
retrieve the quality values. It is possible to open a fastq index as if fasta \ 
(only sequences will be returned), but not the other way round.

New API interfaces to add or update integer, float and array aux tags.

Add level=<number> option to hts_set_opt() to allow the compression level \ 
to be set. Setting level=0 enables uncompressed output.

Improved bgzip error reporting.

Better error reporting when CRAM reference files can't be opened.

Fixes to make tests work properly on Windows/MinGW - mainly to handle line \ 
ending differences.

Efficiency improvements:

Small speed-up for CRAM indexing.

Reduce the number of unnecessary wake-ups in the thread pool.

Avoid some memory copies when writing data, notably for uncompressed BGZF output.

Bug fixes:

Fix multi-region iterator bugs on CRAM files.

Fixed multi-region iterator bug that caused some reads to be skipped incorrectly \ 
when reading BAM files.

Fixed synced_bcf_reader() bug when reading contigs multiple times.

Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when \ 
removing samples.

Fixed bug where the VCF record ref length was calculated incorrectly if an INFO \ 
END tag was present. (71b00a)

Fixed warnings found when compiling with gcc 8.1.0.

sam_hdr_read() and sam_hdr_write() will now return an error code if passed a \ 
NULL file pointer, instead of crashing.

Fixed possible negative array look-up in sam_parse1() that somehow escaped \ 
previous fuzz testing.

Fixed bug where cram range queries could incorrectly report an error when using \ 
multiple threads.

Fixed very rare rANS normalisation bug that could cause an assertion failure \ 
when writing CRAM files.