SAM tools Files

Noteworthy changes in Samtools:

• The sort command creates any needed temporary files alongside the final output file (similarly to the pre-1.3 behaviour), and now aborts when it detects a collision with another sort invocation's temporary files. When the -T PREFIX option specified is a directory (or when sorting to standard output), a random component is now added to temporary filenames to try to avoid collisions (#432, #523, #529, #535, PR #530).
• All samtools commands now check for I/O errors more carefully, especially when writing output files (#111, #253, #470, PR #467).
• Build fixes for 32-bit systems; be sure to run configure on such systems to enable large file support and access to 2GiB+ files.
• The fasta/fastq/bam2fq command no longer ignores reads when the -s option is used (#532).
• The fastq -O option no longer crashes on reads that do not have an OQ tag field (#517).
• The merge and sort commands now handle (unusual) BAM files that have no textual @SQ headers (#548, #550).
• Sorting files containing @CO headers no longer duplicates the comment headers, which previously happened on large sorts for which temporary files were needed (#563).
• The rmdup and view -l commands no longer crash on @RG headers that do not have a LB field (#538).
• Fixed miscellaneous issues #128, #130, #131, #489, and #514.

Noteworthy changes in BCFtools:

• The concat command has a new --naive option for faster operations on large BCFs (PR #359).
• GTisec: new plugin courtesy of David Laehnemann to count genotype intersections across all possible sample subsets in a VCF file.
• Numerous VCF parsing fixes.
• Build fix: peakfit.c now builds correctly with GSL v2 (#378).
• Various bug fixes and improvements to the annotate (#365), call (#366), index (#367), norm (#368, #385), reheader (#356), and roh (#328) commands, and to the fill-tags (#345) and tag2tag (#394) plugins.
• Clarified documentation of view filter options, and of the --regions-file and --targets-file options (#357, #411).

Noteworthy changes in HTSlib:

• Improved error checking and reporting, especially of I/O errors when writing output files (#17, #315, PR #271, PR #317).
• Build fixes for 32-bit systems; be sure to run configure to enable large file support and access to 2GiB+ files.
• Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370). Particular thanks to Kostya Kortchinsky of the Google Security Team for testing and numerous input parsing bug reports.
• HTSlib now prints an informational message when initially creating a CRAM reference cache in the default location under your $HOME directory. (No message is printed if you are using $REF_CACHE to specify a location.)
• Avoided rare race condition when caching downloaded CRAM reference sequence files, by using distinctive names for temporary files (in addition to O_EXCL, which has always been used). Occasional corruption would previously occur when multiple tools were simultaneously caching the same reference sequences on an NFS filesystem that did not support O_EXCL (PR #320).
• Prevented race condition in file access plugin loading (PR #341).
• Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak […] Continue anyway" warning messages (#299).
• Various minor CRAM fixes.

(Numbers in the form #NNN refer to corresponding issue numbers in the relevant GitHub repository.)