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Add latest NEWS for 1.19
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daviesrob committed Dec 11, 2023
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14 changes: 10 additions & 4 deletions NEWS.md
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Expand Up @@ -17,8 +17,7 @@ New work and changes:
read not matching the specified files.
(PR #1896, fixes #1895. Suggested by Feng Tian)

* Cope with Htslib's change to no longer close stdout on is hts_close is
used with the output file being stdout.
* Cope with Htslib's change to no longer close stdout on hts_close.
Htslib companion PR is samtools/htslib#1665.
(PR #1909. Thanks to John Marshall)

Expand All @@ -33,7 +32,7 @@ New work and changes:
(PR #1222, PR #1933, fixes #1758. Thanks to Valeriu Ohan, suggested by
Scott Norton)

Bug Fixes
Bug Fixes:

* Samtools stats: empty barcode tags are now treated as having no barcode.
(PR #1929, fixes #1926. Reported by Jukka Matilainen)
Expand All @@ -43,8 +42,15 @@ Bug Fixes
non-seekable such as stdin or a pipe.
(PR #1930, fixes #1731. Reported by Julian Hess)

* Samtools mpileup -aa (absolutely all positions) now produces an output
even when given an empty input file.
(PR #1939. Reported by Chang Y)

* Samtools markdup: speed up optical duplicate tagging on regions with very
deep data.
(PR #1952)

Documentation
Documentation:

* Samtools mpileup: add more usage examples to the man page.
(PR #1913, fixes #1801)
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