magicDGS ReadTools issues

magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms

https://magicdgs.github.io/ReadTools/

MIT License

6 stars 3 forks source link

issues

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TrimReads for popoolation error

#534 r-mashoodh opened 2 years ago
0
How to extract the UMI info in illumina read's name into a seperate tag

#533 TendoLiu opened 4 years ago
1
spurious assignment of read groups by barcodes with '+' delimiter

#532 AnnaMariaL closed 5 years ago
7
GemMappabilityToBed has problems with some invalid characters in mappability files

#531 robmaz opened 5 years ago
1
DownloadDistmapResult fails with many parts

#530 robmaz opened 5 years ago
1
Release 1.5.2

#529 magicDGS closed 5 years ago
1
Update CHANGELOG

#528 magicDGS closed 5 years ago
1
Remove unused imports

#527 magicDGS closed 5 years ago
2
Use quoted split pattern for barcodes

#526 magicDGS closed 5 years ago
1
Default barcode separators should be treated separately for split

#525 magicDGS closed 5 years ago
2
Specify that the property for default barcode separator is a regexp

#524 magicDGS closed 5 years ago
1
Release 1.5.1

#523 magicDGS closed 5 years ago
1
Update CHANGELOG

#522 magicDGS closed 5 years ago
1
Clean up code and fix typos

#521 magicDGS closed 5 years ago
2
Barcode file with empty header throws user error

#520 magicDGS closed 5 years ago
2
Allow Casava formatted read names with barcode separators

#519 magicDGS closed 5 years ago
1
Better support for read groups in distmap integration

#518 magicDGS opened 5 years ago
1
Add stacktrace always to unexpected errors

#517 magicDGS closed 5 years ago
1
Fix SRA Handbook link

#516 magicDGS closed 5 years ago
1
Create a way to identify issues for beginners/newcomers

#515 magicDGS opened 5 years ago
0
Add stacktrace to unexpected errors

#514 magicDGS closed 5 years ago
0
Better error message for malformed header in barcode file

#513 magicDGS closed 5 years ago
0
Support mixed dual/single indexed files in AssignReadGroupByBarcode

#512 magicDGS opened 5 years ago
9
DownloadDistmapResult: merge SAM header (feature request)

#511 robmaz closed 5 years ago
3
ReadsToDistmap: dump sam header somewhere (feature request)

#510 robmaz closed 5 years ago
4
AssignReadGroupByBarcode: problem with doubly-barcoded reads

#509 robmaz closed 5 years ago
6
ReadsToDistmap: do not require maxReadLength

#508 robmaz opened 5 years ago
2
Decide new theme or create one for help pages

#507 magicDGS opened 5 years ago
0
Migrate docs to its own repository (or gh-pages branch)

#506 magicDGS opened 5 years ago
0
Move javadoc documentation to a service (or gh-pages branch)

#505 magicDGS opened 5 years ago
1
Start publishing ReadTools versions in maven central

#504 magicDGS opened 5 years ago
3
Update CHANGELOG with latest commits

#503 magicDGS closed 5 years ago
1
Improve help for cli calling removed tools

#502 magicDGS closed 5 years ago
1
Upgrade gradle to 4.9 and improve build

#501 magicDGS closed 5 years ago
1
Correct sequence position for char error in GemMappabilityReader

#500 magicDGS closed 5 years ago
2
Experimental GemMappabilityToBed does not work with a real dataset

#499 magicDGS closed 5 years ago
2
Add support for indexing GemMappabilityToBed output

#498 magicDGS opened 5 years ago
0
Release 1.5.0

#497 magicDGS closed 5 years ago
1
Update CHANGELOG before release

#496 magicDGS closed 5 years ago
0
Create tmp directory in scripts/prepare_release.sh

#495 magicDGS closed 5 years ago
0
Add GemScoreMethod for "mappability sensu stricto"

#494 magicDGS opened 5 years ago
0
Create factory for IO stream creation to be used reads but also other files

#493 magicDGS opened 5 years ago
0
Update CHANGELOG with latest changes

#492 magicDGS closed 5 years ago
1
Implement experimental GemMappabilityToBed tool

#491 magicDGS closed 5 years ago
1
Update site dependencies

#490 magicDGS closed 5 years ago
1
Support block-compressed FASTA reference

#489 magicDGS opened 5 years ago
0
Implement deprecated tool registry to better error message if requested

#488 magicDGS closed 5 years ago
0
Upgrade GATK to 4.0.6.0 and htsjdk to 2.16.0

#487 magicDGS closed 5 years ago
2
Investigate performance of buffering for GemMappabilityReader

#486 magicDGS opened 5 years ago
0
Force locale for base test class

#485 magicDGS closed 5 years ago
1