Commits · d9797817aa7b981821ff6465543a2bb9ea499f2b · github_fork / Chromap · GitLab

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Jun 14, 2025
- Significantly improve the scalability by parsing input fastq files in parallel · d9797817
  mourisl authored Jun 14, 2025
  
  d9797817
Jun 12, 2025
- Bump up version · 85e71755
  mourisl authored Jun 11, 2025
  
  85e71755
Jun 05, 2025
- Fix an issue of keeping wrong mapq read during deduplication · 76a51257
  mourisl authored Jun 04, 2025
  
  76a51257
Jun 01, 2025
- Fix a serious issue of comparing SAM mapping record that causes paired-end dedup errors · f3b27b9d
  mourisl authored Jun 01, 2025
  
  f3b27b9d
May 08, 2025
- Update readme to clarify some details about the QC metrics · 06aacab5
  mourisl authored May 07, 2025
  
  View commits for tag v0.3.0 v0.3.0
  
  06aacab5
- bump version number · 18656dd5
  oma219 authored May 07, 2025
  
  18656dd5
- removed reduction for cache_hits_per_batch variable to avoid compilation issue · 0b9ab832
  oma219 authored May 07, 2025
  
  0b9ab832
- update parameters to correct ones for logit model · 478eb198
  oma219 authored Dec 14, 2024
  
  478eb198
- updated parameters for logit function; add inverse logit when printing summary · 40448f9c
  oma219 authored Dec 13, 2024
  
  40448f9c
- hide some cache-related options in the developmental options section · aaa0a809
  oma219 authored Nov 14, 2024
  
  aaa0a809
- removed the --use-all-reads option · d2335ebd
  oma219 authored Nov 14, 2024
  
  d2335ebd
- fix small typo in README · 73cc0f35
  oma219 authored Nov 12, 2024
  
  73cc0f35
- updated README with summary file information · e2435e26
  oma219 authored Nov 12, 2024
  
  e2435e26
- added debug code to print out caceh stats at end of execution · 86b81ed4
  oma219 authored Nov 12, 2024
  
  86b81ed4
- add check in output to make avoid NaNs in summary file · e37d54df
  oma219 authored Nov 12, 2024
  
  e37d54df
- fixed bug with cardinality estimation when sketch is not completely full · df293b89
  oma219 authored Nov 12, 2024
  
  df293b89
- added options/code for num cache slots computation/turned it on by default/outputs in summary file · 5d34dcc0
  oma219 authored Nov 12, 2024
  
  5d34dcc0
- added option for frip est. params/compute est. frip for every barcode/include in summary file · 63b06d3b
  oma219 authored Nov 12, 2024
  
  63b06d3b
- added debug code and options/added cache size, cache param, all reads... · 083a20c4
  oma219 authored Nov 12, 2024
  083a20c4
Nov 09, 2024
- Fix an issue of MD string, where 0 is inserted between adjacent mismatches and... · 9b016207
  mourisl authored Aug 15, 2024
  View commits for tag v0.2.7 v0.2.7
  
  9b016207
Aug 14, 2024
- Add the row that summarize the number of fragments that can not be barcode corrected · 4673c364
  mourisl authored Aug 07, 2024
  
  4673c364
- Do not count the barcode that is not in the whitelist in the summary · 5e67115d
  mourisl authored Jul 22, 2024
  
  5e67115d
- Add a warning message about temp file size. Decrease the temp file doubling threshold to 850. · 3b55bd45
  mourisl authored Jul 19, 2024
  
  3b55bd45
- max_num_mappings_in_mem when using too many temp files · 2af1986f
  Li authored May 11, 2024
  
  2af1986f
May 11, 2024
- Bump up version number · cac1ff54
  Li authored May 08, 2024
  
  cac1ff54
- Use local directory to hold tempoary files when the output file is to stdout or stderr · c1fff8bc
  Li authored May 08, 2024
  
  c1fff8bc
Mar 26, 2024
- Update manpage link in README.md · 30ec17e1
  swiftgenomics authored Mar 25, 2024
  
  30ec17e1
Jan 31, 2024
- Add some debug information when reading the temporary file · 9e8c9802
  Li authored Jan 25, 2024
  
  View commits for tag v0.2.6 v0.2.6
  
  9e8c9802
- Bump up version number · 37541769
  Li authored Jan 25, 2024
  
  37541769
- Update readme · b2d09093
  Li authored Jan 04, 2024
  
  b2d09093
- Fix a bug in summary the alignment stats when outputing SAM format · 4af36173
  Li authored Dec 25, 2023
  
  4af36173
- Output duplication number in bulk bed format too. · 16792ede
  Li authored Dec 22, 2023
  
  16792ede
Dec 20, 2023
- Add more include for stdint · c68c2996
  Li authored Dec 14, 2023
  
  c68c2996
- Add more include for stdint · 54a190c3
  Li authored Dec 14, 2023
  
  54a190c3
- Move li_dev4's content to li_dev5, including no-sorting read-format, and... · 577cccfd
  Li authored Sep 06, 2023
  577cccfd
Sep 06, 2023
- Update version. · 1b6c2d09
  Swift Genomics authored Aug 29, 2023
  
  1b6c2d09
- Update the README on using wildcards in file names. · 32421540
  Swift Genomics authored Aug 29, 2023
  
  32421540
- Support wildcards in read file names. · 3471243b
  Swift Genomics authored Aug 29, 2023
  
  3471243b
- Use separate functions to add options. · 47dfb47d
  Swift Genomics authored Aug 29, 2023
  
  47dfb47d
- Use a func to add indexing options. · c55b92c9
  Swift Genomics authored Aug 29, 2023
  c55b92c9

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