| HEAD | a5c2e8e | updated based on review | 14 May 2024, 12:11:42 UTC |
| refs/heads/CSIv2 | 84337bd | index: Support for both CSIv1 and CSIv2 | 23 January 2015, 10:45:06 UTC |
| refs/heads/abs-qsum | 90f7ac5 | mpileup: Absolute INFO/QS to allow incremental calling | 24 April 2014, 08:16:07 UTC |
| refs/heads/configure | 9cdce26 | Updated Travis config. It now uses autoconf for htslib and installs the bz2 and lzma library dependencies. TODO: Once we resolve them issing AX_WITH_HTSLIB autoconf macro this will need updating to use autoconf in samtools too. | 01 March 2016, 18:18:54 UTC |
| refs/heads/cram_lossy_names | 853470d | Rewording of input/output options. Given the command line options are --input-fmt-options and --output-fmt-options, it seemed wiser to use the phrases "CRAM input only" and "CRAM output only" when documenting the input/output option strings. It still refers to encoding and decoding elsewhere, but I think this is sufficiently clear. | 01 March 2016, 13:48:58 UTC |
| refs/heads/develop | a5c2e8e | updated based on review | 14 May 2024, 12:11:42 UTC |
| refs/heads/experimental/mpileup-no-vcf | 53f7220 | Remove mpileup VCF/BCF output (which may move to bcftools) Proof-of-concept of removing VCF/BCF output, while leaving pileup-style output here in samtools mpileup. Demonstrates what can be ripped out of bam_plcmd.c and adds an error message to avoid user confusion when a VCF/BCF-specific option is used. | 11 November 2014, 16:14:37 UTC |
| refs/heads/fixes-1.15 | 097ab31 | Add NEWS updates | 28 March 2022, 13:50:43 UTC |
| refs/heads/fixes-1.16 | 0158af5 | Add NEWS items on template-coordinate fixes | 31 August 2022, 16:52:21 UTC |
| refs/heads/ftype | c9ae5d4 | Reflect hts_file_type change in htslib | 08 September 2014, 10:53:02 UTC |
| refs/heads/it | 13b811b | for code backup | 16 November 2012, 18:57:16 UTC |
| refs/heads/master | 906a3b5 | Release 1.20 | 15 April 2024, 14:10:00 UTC |
| refs/heads/mergealign | 01a1e8f | Merge align prototype | 01 February 2024, 17:52:31 UTC |
| refs/heads/standalone | 037bdb1 | Fix control of compression level in bam_merge_core2 (Fixed on develop by 3ef90e939e170880431b880641034c8d78f885b2.) | 12 June 2014, 14:55:19 UTC |
| refs/remotes/git-svn | 6a5b7e3 | Removed SVN ChangeLog; merged my private github Log to ChangeLog.old | 09 March 2012, 02:47:29 UTC |
