https://github.com/bioinfo-pf-curie/mpisort - version-1.9

version-1.9 2023-07-20 - fix a problem during parsing (issue #81) - fix a memory leak (issue #82) - fix bruck part in writeanydim (issue #83)

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Published by fredjarlier over 2 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.8

version 1.8 07/13/2023

• Fix a memory leak in bitonic (issue #77)
• Merge the unmapped reads, now we have only one file when merging (issue #78)
• Change memory allocation in bitonic (issue #79)

Tested on same condition as version 1.7

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Published by fredjarlier over 2 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.7

version-1.7 2023-07-12

- fix merge (issue#73) we remove the samtools dependency and build bam
  unsing bgzip compatible with samtools. Options are the same.
- add hash table collision detection (issue#74)

Tested with

gnu/11.1.0 mpi/openmpi/4.1.4 samtools 1.16.1 (for tests)

on

AMD EPYC 7763 64c

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Published by fredjarlier over 2 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.6

IO improvement. See issue #70.

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Published by fredjarlier over 3 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.5.2

version-1.5.2 2021-03-30 - fix memory leaks (#66) - fix compilation warning (#67)

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Published by fredjarlier almost 4 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.5.1

version-1.5.1 2021-02-27 - fix some memory leaks - fix trouble when compressing very small buffer - review the binding with htslib (see installation guide)

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Published by fredjarlier about 4 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.5

Release mpiSORT 1.5 the 22/01/2022 Lot of things in this release. See the documentation especially for htslib support (tested with htslib 1.14)

• add option in configure for htslib support (--with-libhts) in order to generate a BAM (issue#45)
• add utility script (getSlurmOpt.py) in examples/ to get sbatch option (issue#46)
• add option (-t [uniq, all]) in informaticResources.py (issue#46)
• update mpiSort.c to fit mpiBWAByChr output version-1.3 (issue#47)
• update parser.c with parserpaireduniq function (issue#47)
• option -u of mpiSort takes the chrID as argument (issue#47)
• option -g, -b, -s to generate gzip, bam (need htslib support), sam output (issue#45)
• option -m to produce one sam/bam/gz output file with all chromosoms (issue#52)
• fix a bug during compression of small buffer (issue#49) (thanks to tahashmi for reporting the bug)

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Published by fredjarlier about 4 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.4

version-1.4 2020-10-01 - utilities scripts for informatic resources (getSlurmNodesInfo.sh and informaticResources.py)

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Published by phupe over 5 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.3

version-1.3 2020-07-08 - in case the case of duplicate keys, the sorting algorithm is now stable (i.e two objects with equal keys appear in the same order in sorted output as they appear in the input to be sorted.)

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Published by fredjarlier over 5 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.2

version-1.2 2020-06-29 - fix a run time error

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Published by fredjarlier over 5 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.1

version-1.1 2020-06-09 - release the memory bounds when sorting with power of 2 MPI jobs - fix unbalanced final collective writing - add benchmark part in documentation

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Published by phupe over 5 years ago

https://github.com/bioinfo-pf-curie/mpisort - version-1.0

version-1.0 - mpiSORT: sorts SAM files

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Published by phupe almost 6 years ago