andreas-wilm lofreq3 issues

andreas-wilm / lofreq3

LoFreq Version 3

MIT License

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issues

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Ready to replace lofreq2?

#44 charlesfoster opened 2 years ago
1
No Mark Duplicates mentioned in recommended lofreq v3 pipeline

#43 rahil19 closed 2 years ago
2
Auto-propose filter for snps and indels

#42 andreas-wilm opened 3 years ago
0
Error: unhandled exception: index 89678 not in 0 .. 89677 [IndexDefect]

#41 EmilianaWeiss closed 3 years ago
1
Unit test for indel qualities (correct index)

#40 andreas-wilm opened 3 years ago
1
Region with chr:s-e where s=e not piled up

#39 andreas-wilm opened 3 years ago
0
Not calling insertions on NC_000912_Mpneumoniae

#38 andreas-wilm opened 3 years ago
2
Should indel calling allowed without indel quals?

#37 andreas-wilm opened 3 years ago
0
Add unit tests for SB

#36 andreas-wilm opened 3 years ago
0
Set up tests against simulated NC_000912_Mpneumoniae dataset

#35 andreas-wilm opened 3 years ago
1
PositionData created for all positions on fetched reads, not just within given region

#34 andreas-wilm opened 3 years ago
0
NC_000912_Mpneumoniae: testing affect of viterbi, qualities etc.

#33 andreas-wilm opened 3 years ago
0
Don't even create PositionData for events overlapping (or at least starting) at non-ACGT ref

#32 andreas-wilm opened 3 years ago
0
Setup static binary build

#31 andreas-wilm closed 3 years ago
3
SRR3924583 fails somewhere with IndexDefect

#30 andreas-wilm opened 3 years ago
3
End to end testing (and comparison to old LoFreq) on real data

#29 andreas-wilm opened 3 years ago
0
Mincov and maxcov filter (coverage() function) in the presence of indels

#28 andreas-wilm opened 3 years ago
2
Add unit tests for DP,DP4 vs LoFreq2

#27 andreas-wilm opened 3 years ago
1
Add binary installation notes

#26 andreas-wilm opened 3 years ago
2
Add info on filtering (bcftools recipes, whys...)

#25 andreas-wilm opened 3 years ago
0
Add CI tests

#24 andreas-wilm opened 3 years ago
0
Add FAQ

#23 andreas-wilm opened 3 years ago
0
Performance: Implement parallel processing in other subcommands

#22 andreas-wilm opened 3 years ago
0
Performance: Implement parallel processing in call

#21 andreas-wilm opened 3 years ago
0
Performance: can BAMs be written directly htsnim instead of manually writing SAM

#20 andreas-wilm opened 3 years ago
0
Use GSL approximation for pdf

#19 andreas-wilm opened 3 years ago
0
Ignore non ACGT positions in reference

#18 andreas-wilm closed 3 years ago
2
Add simple logging to subcommands

#17 andreas-wilm opened 3 years ago
0
gatk indel qualities

#16 jeongmeani closed 3 years ago
1
alnqual implemenation missing

#15 andreas-wilm closed 3 years ago
1
Fix len(t) == L` the length of the table changed while iterating over it when cleaning zombie entries in pileup

#14 andreas-wilm closed 4 years ago
1
Build issues, nim reports a type mismatch

#13 jonaudet closed 4 years ago
2
Region offset error

#12 andreas-wilm opened 4 years ago
0
Support BAM reading threads

#11 andreas-wilm closed 4 years ago
1
Fix simple cases of invalid cigars

#10 andreas-wilm opened 4 years ago
1
Infer regions automatically

#9 andreas-wilm closed 3 years ago
1
Optimizations needed: twice as slow as LoFreq2

#8 andreas-wilm opened 4 years ago
3
lofreq and lofreq3 future

#7 nekrut closed 4 years ago
2
Implement caller skipping json printing

#6 andreas-wilm closed 4 years ago
0
Add --min-af to pileup for speedup

#5 andreas-wilm opened 4 years ago
1
INFO 'TYPE' is not defined in vcf header

#4 andreas-wilm closed 4 years ago
0
implement json to samtools pileup converter

#3 andreas-wilm opened 4 years ago
0
deletion bases reported wrongly

#2 andreas-wilm closed 4 years ago
0
DP4 incorrectly reported for indels

#1 andreas-wilm closed 4 years ago
1