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