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Add last-minute NEWS items for release #1833

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Sep 9, 2024
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Add last-minute NEWS items for release #1833

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27 changes: 17 additions & 10 deletions NEWS
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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)
Expand Down Expand Up @@ -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
---------

Expand Down Expand Up @@ -109,16 +117,15 @@ 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)

* 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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Expand Down