Giters
andreas-wilm
/
lofreq3
LoFreq Version 3
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27
Watchers:
3
Issues:
44
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0
andreas-wilm/lofreq3 Issues
Ready to replace lofreq2?
Updated
3 years ago
Comments count
1
No Mark Duplicates mentioned in recommended lofreq v3 pipeline
Closed
3 years ago
Comments count
2
Add binary installation notes
Updated
3 years ago
Comments count
2
Auto-propose filter for snps and indels
Updated
3 years ago
Unit test for indel qualities (correct index)
Updated
3 years ago
Comments count
1
Error: unhandled exception: index 89678 not in 0 .. 89677 [IndexDefect]
Closed
3 years ago
Comments count
1
Not calling insertions on NC_000912_Mpneumoniae
Updated
3 years ago
Comments count
2
Region with chr:s-e where s=e not piled up
Updated
3 years ago
Set up tests against simulated NC_000912_Mpneumoniae dataset
Updated
3 years ago
Comments count
1
Mincov and maxcov filter (coverage() function) in the presence of indels
Updated
3 years ago
Comments count
2
Add unit tests for DP,DP4 vs LoFreq2
Updated
3 years ago
Comments count
1
Should indel calling allowed without indel quals?
Updated
3 years ago
Add unit tests for SB
Updated
3 years ago
End to end testing (and comparison to old LoFreq) on real data
Updated
3 years ago
Infer regions automatically
Closed
3 years ago
Comments count
1
PositionData created for all positions on fetched reads, not just within given region
Updated
3 years ago
Region offset error
Updated
3 years ago
NC_000912_Mpneumoniae: testing affect of viterbi, qualities etc.
Updated
3 years ago
Add info on filtering (bcftools recipes, whys...)
Updated
3 years ago
Setup static binary build
Closed
3 years ago
Comments count
3
SRR3924583 fails somewhere with IndexDefect
Updated
3 years ago
Comments count
3
Ignore non ACGT positions in reference
Closed
3 years ago
Comments count
2
Don't even create PositionData for events overlapping (or at least starting) at non-ACGT ref
Updated
3 years ago
Add FAQ
Updated
3 years ago
Add CI tests
Updated
3 years ago
Performance: Implement parallel processing in other subcommands
Updated
3 years ago
Performance: Implement parallel processing in call
Updated
3 years ago
Performance: can BAMs be written directly htsnim instead of manually writing SAM
Updated
3 years ago
Optimizations needed: twice as slow as LoFreq2
Updated
4 years ago
Comments count
3
Use GSL approximation for pdf
Updated
4 years ago
Add simple logging to subcommands
Updated
4 years ago
alnqual implemenation missing
Closed
4 years ago
Comments count
1
gatk indel qualities
Closed
4 years ago
Comments count
1
Fix len(t) == L` the length of the table changed while iterating over it when cleaning zombie entries in pileup
Closed
4 years ago
Comments count
1
Build issues, nim reports a type mismatch
Closed
4 years ago
Comments count
2
Support BAM reading threads
Closed
5 years ago
Comments count
1
Fix simple cases of invalid cigars
Updated
5 years ago
Comments count
1
INFO 'TYPE' is not defined in vcf header
Closed
5 years ago
Implement caller skipping json printing
Closed
5 years ago
Add --min-af to pileup for speedup
Updated
5 years ago
Comments count
1
lofreq and lofreq3 future
Closed
5 years ago
Comments count
2
implement json to samtools pileup converter
Updated
5 years ago
DP4 incorrectly reported for indels
Closed
5 years ago
Comments count
1
deletion bases reported wrongly
Closed
5 years ago