samtools/samtools 1.4.1

on GitHub

This is primarily a security bug fix update.

• Added options to fastq to create fastq files from BC (or other)
  tags.

• Samtools view has gained a -G option to exclude on all bits
  set. For example to discard reads where neither end has been
  mapped use "-G 12".

• Samtools cat has a -b option to ease concatenation of many
  files.

• Added misc/samtools_tab_completion for bash auto-completion of
  samtools sub-commands. (#560)

• Samtools tview now has J and K keys for verticale movement by 20
  lines. (#257)

• Various compilation / portability improvements.

• Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.
  (#667)

The samtools-1.4.1.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.