samtools/samtools 1.3.1

on GitHub

• 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.

The samtools-1.3.1.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.