@@ -27,13 +27,16 @@ Updates
2727 fraction separately for source and target. (PR #1811)
2828
2929* Added new APIs to facilitate low-level CRAM container manipulations,
30- used by the new "samtools cat" region filtering code. Functions are
31- cram_container_get_coords(), cram_filter_container(),
32- cram_index_extents(), cram_container_num2offset(),
33- cram_num_containers(), cram_num_containers_between(),
34- cram_skip_container().
35- Also improved cram_index_query() and cram_index_query() to cope with
36- HTS_IDX_NOCOOR regions. (PR #1771)
30+ used by the new "samtools cat" region filtering code. Functions are:
31+ cram_container_get_coords()
32+ cram_filter_container()
33+ cram_index_extents()
34+ cram_container_num2offset()
35+ cram_container_offset2num()
36+ cram_num_containers()
37+ cram_num_containers_between()
38+ Also improved cram_index_query() to cope with HTS_IDX_NOCOOR regions.
39+ (PR #1771)
3740
3841* Bgzip now retains file modification and access times when
3942 compressing and decompressing. (PR #1727, fixes #1718. Requested by
@@ -48,6 +51,9 @@ Updates
4851 #1667, PR #1764, PR #1786, PR #1802, thanks to Ruben Vorderman) and
4952 ARM (PR #1795, thanks to John Marshall).
5053
54+ * bgzf_getline() will now warn if it encounters UTF-16 data.
55+ (PR #1487, thanks to John Marshall)
56+
5157* Speed up bgzf_read(). While this does not reduce CPU significantly,
5258 it does increase the maximum parallelism available permitting 10-15%
5359 faster decoding. (PR #1772, PR #1800, Issue #1798)
@@ -75,6 +81,8 @@ Build Changes
7581
7682* Updated htscodecs submodule to version 1.6.1 (PR #1828)
7783
84+ * Fixed an awk script in the Makefile that only worked with gawk. (PR #1831)
85+
7886Bug fixes
7987---------
8088
@@ -109,16 +117,15 @@ Bug fixes
109117 returning overlapping records. (PR #1787. Fixes
110118 samtools/samtools#2060, reported by acorvelo)
111119
112- * Warn in bgzf_getline() encounters UTF-16 data.
113- (PR #1487, thanks to John Marshall)
114-
115120* Replace assert() with abort() in BCF synced reader. This is not an
116121 ideal solution, but it gives consistent behaviour when compiling
117122 with or without NDEBUG. (PR #1791, thanks to Martin Pollard)
118123
119124* Fixed failure to change the write block size on compressed SAM or VCF
120125 files due to an internal type confusion. (PR #1826)
121126
127+ * Fixed an out-of-bounds read in cram_codec_iter_next() (PR #1832)
128+
122129Noteworthy changes in release 1.20 (15th April 2024)
123130~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
124131
0 commit comments