Download the source code here: samtools-1.19.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)
Bug Fixes:
-
Fixed a possible array bounds violation when looking up regions in a BED file (e.g. using
samtools view -L). This could lead to crashes or the return of incomplete results if the BED file contained a large number of entries all referencing low positions on a chromosome. (PR #1962, fixes #1961. Reported by geertvandeweyer) -
Fixed a crash in samtools stats that occurred when trying to clean up after it was unable to open a CRAM reference file. (PR #1957, fixes crash reported in samtools/htslib#1723. Reported by Alex Leonard)
Documentation: -
Fixed inverted logic in the
samtools consensus --show-delmanual page description. (PR #1955, fixes #1951. Reported by Mikhail Schelkunov) -
Added a description of the MPC section to the
samtools statsmanual page. (PR #1963, fixes #1954. Reported by litun-fkby)