Log Message:
samtools: updated to 1.16.1

1.16.1

Bug fixes:

Fixed a bug with the template-coordinate sort which caused incorrect ordering \ 
when using threads, or processing large files that don't fit completely in \ 
memory.

Fixed a crash that occurred when trying to use samtools merge in \ 
template-coordinate mode.

1.16

New work and changes:

samtools reference command added. This subcommand extracts the embedded \ 
reference out of a CRAM file.

samtools import now adds grouped by query-name to the header.

Made samtools view read error messages more generic. Former error message would \ 
claim that there was a "truncated file or corrupt BAM index file" with \ 
no real justification. Also reset errno in stream_view which could lead to \ 
confusing error messages.

Make samtools view -p also clear mqual, tlen and cigar.

Add bedcov option -c to report read count.

Add UMI/barcode handling to samtools markdup.

Add a new template coordinate sort order to samtools sort and samtools merge. \ 
This is useful when working with unique molecular identifiers (UMIs).

Rename mpileup --ignore-overlaps to --ignore-overlaps-removal or \ 
--disable-overlap-removal. The previous name was ambiguous and was often read as \ 
an option to enable removal of overlapping bases, while in reality this is on by \ 
default and the option turns off the ability to remove overlapping bases.

The dict command can now read BWA's .alt file and add AH:* tags indicating \ 
reference sequences that represent alternate loci.

The samtools index command can now accept multiple alignment filenames with the \ 
new -M option, and will index each of them separately. (Specifying the output \ 
index filename via out.index or the new -o option is currently only applicable \ 
when there is only one alignment file to be indexed.)

Allow samtools fastq -T "*". This allows all tags from SAM records to \ 
be written to fastq headers. This is a counterpart to samtools import -T \ 
"*".

Bug Fixes:

Re-enable --reference option for samtools depth. The reference is not used but \ 
this makes the command line usage compatible with older releases.

Fix regex coordinate bug in samtools markdup.

Fix divide by zero in plot-bamstats -m, on unmapped data.

Fix missing RG headers when using samtools merge -r.

Fix a possible unaligned access in samtools reference.

Documentation:

Add documentation on CRAM compression profiles and some of the newer options \ 
that appear in CRAM 3.1 and above.

Add sclen filter expression keyword documentation.

Extend FILTER EXPRESSION man page section to match the changes made in HTSlib.

Non user-visible changes and build improvements:

Ensure generated test files are ignored (by git) and cleaned (by make testclean)