immcantation presto issues

immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.

https://presto.readthedocs.io

GNU Affero General Public License v3.0

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issues

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Add ParseHeaders mode to copy multiple annotations into one

#44 ssnn-airr closed 6 years ago
1
Verify vsearch compatibility

#43 ssnn-airr closed 7 years ago
3
MaskPrimers-align edge cases are not masking correctly

#42 ssnn-airr opened 8 years ago
6
MaskPrimers throws "Error in sibling process detected" errors during Illumina MiSeq 2x250 BCR mRNA example

#41 ssnn-airr closed 6 years ago
6
Error with Greiff2014 V primers example

#40 ssnn-airr closed 8 years ago
1
Add select to SplitSeq

#39 ssnn-airr closed 7 years ago
5
Verify installation using setup.py works in Windows

#38 ssnn-airr closed 8 years ago
2
Separate required and option arguments in help

#37 ssnn-airr closed 7 years ago
1
Check if we can use the sequence description for the id

#36 ssnn-airr closed 6 years ago
1
Windows sdist won't install due to junk in SOURCES.txt

#35 ssnn-airr closed 8 years ago
1
Add ENA header support

#34 ssnn-airr closed 6 years ago
1
Add option to rename MaskPrimers output fields

#33 ssnn-airr closed 6 years ago
2
Add collapse action flag to PairSeq

#32 ssnn-airr closed 6 years ago
1
Add sniff mode to ConvertHeaders

#31 ssnn-airr closed 6 years ago
1
Update options in examples

#30 ssnn-airr closed 8 years ago
4
Convert README to restructuredText

#29 ssnn-airr closed 9 years ago
2
Added output filename argument

#28 ssnn-airr closed 6 years ago
2
Add subcommand to ParseHeader that merges fields

#27 ssnn-airr closed 9 years ago
1
Added error and median quality filters

#26 ssnn-airr closed 6 years ago
1
Add support for input of gzip files and/or stdin

#25 ssnn-airr closed 6 years ago
2
CollapseSeq on MakeDb

#24 ssnn-airr closed 9 years ago
2
Need UID clustering script

#23 ssnn-airr closed 6 years ago
3
tests failing (before and after python3 conversion)

#22 ssnn-airr closed 9 years ago
3
Check pip version in setup.py

#21 ssnn-airr closed 9 years ago
1
maskPrimers gapped alignment penalties

#20 ssnn-airr closed 9 years ago
4
Change --maxmiss in BuildConsensus to only gap characters.

#19 ssnn-airr closed 9 years ago
1
diversity calculation quality-aware ?

#18 ssnn-airr closed 9 years ago
14
Check for usearch and muscle in PATH first

#17 ssnn-airr closed 7 years ago
1
Reduce multiprocessing overhead

#16 ssnn-airr opened 9 years ago
3
error during AlignSets

#15 ssnn-airr closed 6 years ago
20
Restore pair-fail files in PairSeq

#14 ssnn-airr closed 9 years ago
1
AssemblePairs-reference : option to fill in nt from reference for gapped stitch

#13 ssnn-airr closed 8 years ago
7
minlen capability with MaskPrimers

#12 ssnn-airr closed 6 years ago
2
Add concatenate action to ParseHeaders-collapse

#11 ssnn-airr closed 9 years ago
1
"READS" in DefineClones log

#10 ssnn-airr closed 9 years ago
2
no automatic line wrap on fasta

#9 ssnn-airr closed 6 years ago
5
flag/capability for BuildConsensus to keep certain fields

#8 ssnn-airr closed 9 years ago
2
Autogenerate commandline reference documentation with Sphinx

#7 ssnn-airr closed 9 years ago
1
Improve sibling process exception checking

#6 ssnn-airr opened 9 years ago
1
AlignSets.py fatal error in write() command (with core dump )

#5 ssnn-airr closed 9 years ago
2
Update package to Python 3 compatibility

#4 ssnn-airr closed 9 years ago
1
BuildConsensus log output doesn't convey --maxmiss results

#3 ssnn-airr closed 9 years ago
1
MaskPrimers primer alignment log not displaying indels correctly

#2 ssnn-airr closed 9 years ago
1
PairSeq is slow on large files

#1 ssnn-airr closed 9 years ago
2