collaborativebioinformatics STRdust issues

collaborativebioinformatics / STRdust

MIT License

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issues

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Rotate nucleotides in output

#51 wdecoster opened 3 years ago
0
Properly sort chromosomes in output file

#50 wdecoster opened 3 years ago
0
dustspec.split("'")[1].split("_") fails with decoy contigs

#49 wdecoster opened 3 years ago
1
How do sequences end up being empty?

#48 wdecoster opened 3 years ago
0
_validate_path writes a 'test' directory

#47 wdecoster opened 3 years ago
0
Parallelization

#46 wdecoster closed 3 years ago
0
setup CI

#45 wdecoster opened 3 years ago
0
Test data

#44 lfpaulin closed 3 years ago
0
Addition of test data and removal of previous dataset

#43 lfpaulin closed 3 years ago
0
Simulation strategy - README

#42 lfpaulin closed 3 years ago
0
Simulation strategy

#41 lfpaulin closed 3 years ago
0
output number of reads supporting a call

#40 wdecoster opened 3 years ago
1
some changes

#39 wdecoster closed 3 years ago
0
error in parse_mreps_result

#38 wdecoster closed 3 years ago
1
Adding some fancy stuff.

#37 PavelAvdeyev closed 3 years ago
0
dict.update rather than looping over keys?

#36 wdecoster closed 3 years ago
0
Not crucial now: output to VCF while running

#35 wdecoster opened 3 years ago
1
Not crucial now, but could we have the --ins_file option default to a tmpfile?

#34 wdecoster closed 3 years ago
1
Find heuristics to pre-filter insertions that we don't want spoa to spend too much time on

#33 wdecoster opened 3 years ago
4
Code avdeev

#32 PavelAvdeyev closed 3 years ago
1
Github - Methods + Results

#31 lfpaulin opened 3 years ago
0
Github : Add simulation strategy

#30 lfpaulin closed 3 years ago
2
Analysis: how good is STRdust

#29 lfpaulin opened 3 years ago
0
Github: add how to install

#28 lfpaulin opened 3 years ago
1
Github - Add how to run

#27 lfpaulin closed 3 years ago
1
Update sequence length

#26 lfpaulin closed 3 years ago
0
strdust now creates output

#25 lfpaulin closed 3 years ago
0
add run mreps, and test data

#24 lfpaulin closed 3 years ago
0
potential bug in merge_overlapping_insertions

#23 PavelAvdeyev closed 3 years ago
0
Test STRdust to human and/or tomato data

#22 lfpaulin opened 3 years ago
0
Test STRdust installation

#21 lfpaulin closed 3 years ago
3
Take one or a few simulated STRs and see if the output makes sense!

#20 wdecoster opened 3 years ago
2
bonus: add parallelization

#19 wdecoster opened 3 years ago
0
Add logging to script

#18 wdecoster closed 3 years ago
1
Write code to create output file

#17 wdecoster closed 3 years ago
2
Add mreps to check repetiviness (is that a word?) of consensus sequence

#16 wdecoster closed 3 years ago
5
Coding part1

#15 wdecoster closed 3 years ago
0
Coding part1

#14 wdecoster closed 3 years ago
0
Review function horizontal_merge()

#13 wdecoster opened 3 years ago
1
Pipeline dev

#12 lfpaulin closed 3 years ago
0
Gather suggestions for name, figure out which ones do not exist, and make a poll

#11 wdecoster closed 3 years ago
1
SURVIVOR and minimap2 scripts

#10 lfpaulin closed 3 years ago
3
Adding flow chart

#9 wdecoster closed 3 years ago
0
Run tricolor on our simulated data

#8 wdecoster opened 3 years ago
2
Run straglr on simulated data

#7 wdecoster opened 3 years ago
2
Upload non-simulated quick test phased bam

#6 wdecoster closed 3 years ago
2
Write code to extract insertions and softclips per haplotype

#5 wdecoster closed 3 years ago
1
Create phased BAM

#4 wdecoster closed 3 years ago
1
Create simulated reads based on simulated genomes with new STR genotypes

#3 wdecoster closed 3 years ago
2
Convert annotation of STRs to bed format

#2 wdecoster closed 3 years ago
1