karel-brinda ococo issues

karel-brinda / ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

https://arxiv.org/abs/1712.01146

MIT License

47 stars 3 forks source link

issues

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Add the option to redirect the new consensus to the standard output by `-F -`

#39 karel-brinda opened 1 year ago
0
consensus file has header of reference and not name bam/sample file

#38 MarinaSci closed 1 year ago
5
use in hybrid assembly

#37 phiweger opened 5 years ago
1
Add an analogy of samtools depth

#36 karel-brinda opened 5 years ago
0
Use SVG in readme

#35 karel-brinda closed 6 years ago
0
Ococo 0.1.2.7

#34 karel-brinda closed 5 years ago
0
Automatically regenerate the how-to section

#33 karel-brinda closed 6 years ago
0
VCF with both SNV and non SNV's

#32 Takadonet opened 6 years ago
3
Include deletion events in VCF

#31 Takadonet opened 6 years ago
3
Coverage filter

#30 karel-brinda opened 6 years ago
0
Review galaxy wrapper

#29 Takadonet closed 6 years ago
1
Upgrade version in code

#28 Takadonet closed 6 years ago
1
Test all combinations of parameters

#27 karel-brinda opened 6 years ago
0
Tool cannot run --maj-thres flag

#26 Takadonet closed 6 years ago
1
Download submodule

#25 karel-brinda closed 6 years ago
0
Fix tests

#24 karel-brinda closed 6 years ago
0
Ococo man install procedure breaks Conda

#23 karel-brinda closed 6 years ago
1
Filtration by flags

#22 karel-brinda opened 8 years ago
0
Assertion `psu.sum < max_depth' failed.

#21 karel-brinda closed 5 years ago
1
Segmentation fault when read exceeds reference boundaries

#20 karel-brinda opened 8 years ago
0
Ococo 0.1.2

#19 karel-brinda closed 8 years ago
0
FASTA output represents ambiguity with '=' chars rather than Ns

#18 bede closed 8 years ago
1
Add allele frequency to VCF output

#17 karel-brinda closed 8 years ago
0
Allele frequency

#16 karel-brinda closed 8 years ago
4
Flag for exact coverage

#15 karel-brinda opened 8 years ago
0
How do you interpret the output?

#14 george-githinji closed 8 years ago
11
Simplified compilation

#13 karel-brinda closed 8 years ago
0
Travis

#12 karel-brinda closed 8 years ago
0
Potential licensing issue

#11 karel-brinda closed 8 years ago
0
Error message when several outputs are redirected to standard output

#10 karel-brinda closed 8 years ago
0
Wrong dynamic linking of Boost on some machines

#9 karel-brinda closed 8 years ago
1
Devel

#8 karel-brinda closed 8 years ago
0
Counter size selection using command-line parameters

#7 karel-brinda closed 8 years ago
0
Add verbose mode

#6 karel-brinda closed 8 years ago
0
Add stat view mode (to display statistics in an ococo file)

#5 karel-brinda closed 8 years ago
0
Major update

#4 karel-brinda closed 8 years ago
0
Usage in a mapper

#3 karel-brinda closed 8 years ago
1
Parameter for specification of chromosomes

#2 karel-brinda closed 5 years ago
0
CLI tests

#1 karel-brinda closed 8 years ago
0