Summer 2021 NEWS update #1303
Summer 2021 NEWS update #1303
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whitwham
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Co-authored-by: John Marshall <jmarshall@hey.com>
NEWS
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| * Prevent assert in bcf_sr_set_regions. Thanks to Dr K D Murray. | ||
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| * Fixed the update of the minimum offset when unmapped reads are present. This |
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This is a serious bug that should be more clearly described, placed at the top of the list, and probably noted in samtools's NEWS as well. Perhaps something like
Fixed
hts_itr_query()et al region queries: fixed bug introduced in HTSlib 1.12, which lead to iterators producing very few reads for some queries (especially for larger target regions) when unmapped reads were present. (HTSlib 1.11 had a related problem in which iterators would omit a few unmapped reads that should have been produced; cf #1142.)
This has probably been reported multiple times: #1279 as listed (first and best researched, so the credit for Daniel is certainly deserved), but also samtools/samtools#1451, possibly #1290, probably #1305 and samtools/samtools#1457, and perhaps samtools/samtools#1460.
Over in samtools, this could be described in terms of region queries instead:
Fixed
samtools view FILE REGIONandmpileup -r REGIONetc region queries: fixed bug introduced in 1.12, which lead to region queries producing very few reads for […]
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Thanks for applying. It'd probably be worth listing the additional bug report numbers, and I'm afraid it should be s/lead/led/ — I'm pretty good at mixing that one up 😄
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Perhaps the other bug reports should be mentioned in the SAMtools news, as they are related to running samtools commands.
NEWS
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| number of contigs from an index. | ||
| (#1295 and #1299) | ||
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| * Added bracket handling to bcf_hdr_parse_line. Thanks to Alberto Casas Orrtiz. |
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| * Added bracket handling to bcf_hdr_parse_line. Thanks to Alberto Casas Orrtiz. | |
| * Added bracket handling to bcf_hdr_parse_line. Thanks to Alberto Casas Ortiz. |
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Good catch. I'm too heavy on the 'R' key.
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I will update my latest commit to fix this.
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(More for the trivia commit: there were a few trailing spaces near the Hulselmans entry too.)
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Add a little more explanation, and try to describe the outcome of some of the changes for end users.
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I've added a few adjustments, to better describe the outcome of some of the changes listed from an end-user perspective. |
Please take a look for errors, omissions or entirely fictional updates.
This will be kept updated until we are ready for a release.