Commits · 9f64fc39dabe3d4bf36f0221eee97998db8ff91d · FONDA_A6 / popins4snake

Aug 09, 2024
- Making minimum length requirement of reads in crop_unmapped after base quality... · 9f64fc39
  Birte Kehr authored 7 months ago
```
Making minimum length requirement of reads in crop_unmapped after base quality trimming a parameter.
```
  9f64fc39
Aug 01, 2024
- Adding option for setting the minimum base qualities of reads to be cropped for unmapped assembly. · b55253e6
  Birte Kehr authored 8 months ago
  
  b55253e6
Dec 06, 2023
- Adding total read count in BAM file to POPINS_SAMPLE_INFO file instead of command line. · 456a287b
  Birte Kehr authored 1 year ago
  
  456a287b
- Adding total read count in BAM file to command line output. · 572f3abf
  Birte Kehr authored 1 year ago
  
  572f3abf
Sep 01, 2022
- Fixing Nat Genet referenceand link to journal in README.md. · 8720de82
  Birte Kehr authored 2 years ago
  
  8720de82
- Simplifying dependency on Bifrost installation. · b9b5f50a
  Birte Kehr authored 2 years ago
  
  b9b5f50a
Aug 25, 2022
- More edits to README - command descriptions still incomplete. · 006b9184
  Birte Kehr authored 2 years ago
  
  006b9184
- Updating version information. · 366363ae
  Birte Kehr authored 2 years ago
  
  366363ae
- Edited README - command descriptions still incomplete. · 32c9fa8a
  Birte Kehr authored 2 years ago
  
  32c9fa8a
- Adding back an option to suppress printing the POPINS_SAMPLE_INFO file. · 2fa1d422
  Birte Kehr authored 2 years ago
  
  2fa1d422
- Replacing popins2 by popins4snake in status messages. · a52d4f57
  Birte Kehr authored 2 years ago
  
  a52d4f57
Aug 18, 2022

Cleaning popins4snake code, in particular the argument parser. Introducing a... · 811a2af7

Birte Kehr authored 2 years ago

Cleaning popins4snake code, in particular the argument parser. Introducing a merge-locations command by splitting this task from place-refalign.

811a2af7

Aug 16, 2022
- Removing .gitignore from .gitignore. · 939035af
  Birte Kehr authored 2 years ago
  
  939035af
- Adding .gitignore file. · 2e4d6160
  Birte Kehr authored 2 years ago
  
  2e4d6160
- Cleaning unused PopIns2 leftovers from popins4snake code. · 0987ec38
  Birte Kehr authored 2 years ago
  
  0987ec38
Mar 18, 2022
- Merge branch 'fix-sam-format-PG-IDs' into 'main' · 56ae3fc5
  Kedi Cao authored 3 years ago
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Fix duplication of PG IDs when merging SAM headers

See merge request !8
```
  56ae3fc5
Mar 17, 2022
- fixed duplication issue in PG ID fields · ed82221d
  Thomas Krannich authored 3 years ago
  
  ed82221d
- fix atoi, as it's not part of gcc · 14382801
  Thomas Krannich authored 3 years ago
  
  14382801
- Merge branch 'fix-sam-format-PG-IDs' of... · 2c94217e
  Thomas Krannich authored 3 years ago
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Merge branch 'fix-sam-format-PG-IDs' of https://gitlab.informatik.hu-berlin.de/fonda_a6/popins4snake into fix-sam-format-PG-IDs
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  2c94217e
- update PG IDs fields · 5e684d39
  Thomas Krannich authored 3 years ago
  
  5e684d39
Mar 16, 2022
- Merge branch 'main' into 'fix-sam-format-PG-IDs' · c3e1cbdc
  Thomas Krannich authored 3 years ago
```
# Conflicts:
#   Makefile
```
  c3e1cbdc
- improved conflict solving for duplicated PG IDs when merging SAM headers · 84f646a1
  Thomas Krannich authored 3 years ago
  
  84f646a1
- Merge branch 'fix-find-locations-io' into 'main' · 45801564
  Kedi Cao authored 3 years ago
```
fixing file existence check

See merge request !7
```
  45801564
- fixing file existence check · 94523d1e
  Thomas Krannich authored 3 years ago
  
  94523d1e
- Merge branch 'fix-find-locations-io' into 'main' · 8ca524d9
  Kedi Cao authored 3 years ago
```
add IO of non-ref alignment file name

See merge request !6
```
  8ca524d9
- add IO of non-ref alignment file name · 21a8baad
  Thomas Krannich authored 3 years ago
  
  21a8baad
Mar 15, 2022
- initial change to see if SAM/BAM headers are modified · 6e245391
  Thomas Krannich authored 3 years ago
  
  6e245391
Mar 10, 2022
- Merge branch 'fix-crop-unmapped-io' into 'main' · b740c065
  Kedi Cao authored 3 years ago
```
crop-unmapped with even more flexibility of the input parameters, se, pe1, pe2

See merge request !5
```
  b740c065
- crop-unmapped with even more flexibility of the input parameters, se, pe1, pe2 · 8912e43c
  Thomas Krannich authored 3 years ago
  
  8912e43c
Jan 20, 2022
- Merge branch 'fix-crop-unmapped-io' into 'main' · 699eb849
  Kedi Cao authored 3 years ago
```
new I/O for the crop-unmapped module

See merge request !4
```
  699eb849
- new I/O for the crop-unmapped module · 46c6651d
  Thomas Krannich authored 3 years ago
  
  46c6651d
- fix conflict after merge · 275bb741
  kdc715 authored 3 years ago
  
  275bb741
- Merge branch 'main' of https://gitlab.informatik.hu-berlin.de/fonda_a6/popins4snake into main · 3decf084
  kdc715 authored 3 years ago
  
  3decf084
- Merge branch 'new-find-locations-module' into 'main' · 3c91fa0f
  Kedi Cao authored 3 years ago
```
new find-locations module

See merge request !3
```
  3c91fa0f
Jan 19, 2022
- new find-locations module · 39a43351
  Thomas Krannich authored 3 years ago
  
  39a43351
Dec 16, 2021
- Merge branch 'ext-krannich-main-patch-38442' into 'main' · 835eeb5f
  Kedi Cao authored 3 years ago
```
fix argument check in parser of merge-and-set-mate

See merge request !2
```
  835eeb5f
Dec 15, 2021
- updating merge-set-mate function, tested with simulated data · fbe82007
  kdc715 authored 3 years ago
  
  fbe82007
Dec 10, 2021
- fix argument check in parser of merge-and-set-mate · e237334e
  Thomas Krannich authored 3 years ago
  
  e237334e
Dec 09, 2021
- Merge branch 'merge-and-set-mate' into 'main' · 8b2c1833
  Kedi Cao authored 3 years ago
```
innitial rework of popins2 merge and setmate module

See merge request !1
```
  8b2c1833
Dec 06, 2021
- innitial rework of popins2 merge and setmate module · 6cd8d525
  Krannich479 authored 3 years ago
  
  6cd8d525