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.


(adam)