From bf118051d99ceebcf7809033d2aa00a68f107456 Mon Sep 17 00:00:00 2001 From: Rob Davies Date: Mon, 9 Sep 2024 09:25:48 +0100 Subject: [PATCH] Add last-minute NEWS items for release --- NEWS | 27 +++++++++++++++++---------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/NEWS b/NEWS index e6962e25f..be8de6682 100644 --- a/NEWS +++ b/NEWS @@ -27,13 +27,16 @@ Updates fraction separately for source and target. (PR #1811) * Added new APIs to facilitate low-level CRAM container manipulations, - used by the new "samtools cat" region filtering code. Functions are - cram_container_get_coords(), cram_filter_container(), - cram_index_extents(), cram_container_num2offset(), - cram_num_containers(), cram_num_containers_between(), - cram_skip_container(). - Also improved cram_index_query() and cram_index_query() to cope with - HTS_IDX_NOCOOR regions. (PR #1771) + used by the new "samtools cat" region filtering code. Functions are: + cram_container_get_coords() + cram_filter_container() + cram_index_extents() + cram_container_num2offset() + cram_container_offset2num() + cram_num_containers() + cram_num_containers_between() + Also improved cram_index_query() to cope with HTS_IDX_NOCOOR regions. + (PR #1771) * Bgzip now retains file modification and access times when compressing and decompressing. (PR #1727, fixes #1718. Requested by @@ -48,6 +51,9 @@ Updates #1667, PR #1764, PR #1786, PR #1802, thanks to Ruben Vorderman) and ARM (PR #1795, thanks to John Marshall). +* bgzf_getline() will now warn if it encounters UTF-16 data. + (PR #1487, thanks to John Marshall) + * Speed up bgzf_read(). While this does not reduce CPU significantly, it does increase the maximum parallelism available permitting 10-15% faster decoding. (PR #1772, PR #1800, Issue #1798) @@ -75,6 +81,8 @@ Build Changes * Updated htscodecs submodule to version 1.6.1 (PR #1828) +* Fixed an awk script in the Makefile that only worked with gawk. (PR #1831) + Bug fixes --------- @@ -109,9 +117,6 @@ Bug fixes returning overlapping records. (PR #1787. Fixes samtools/samtools#2060, reported by acorvelo) -* Warn in bgzf_getline() encounters UTF-16 data. - (PR #1487, thanks to John Marshall) - * Replace assert() with abort() in BCF synced reader. This is not an ideal solution, but it gives consistent behaviour when compiling with or without NDEBUG. (PR #1791, thanks to Martin Pollard) @@ -119,6 +124,8 @@ Bug fixes * Fixed failure to change the write block size on compressed SAM or VCF files due to an internal type confusion. (PR #1826) +* Fixed an out-of-bounds read in cram_codec_iter_next() (PR #1832) + Noteworthy changes in release 1.20 (15th April 2024) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~