Comments (10)
yes, just use --sex ''
and it will understand. it defaults to --sex X,Y
so you have to explicitly give it the empty string.
from goleft.
Ok, cheers. I tried that before but thought that led to the error.
goleft_linux64 indexcov -d indexcov --sex '' *.bam
2018/04/19 17:16:49 indexcov: running on 50 indexes
2018/04/19 17:16:49 sex chromosomes not found.
2018/04/19 17:16:49 got: 0 principal components
2018/04/19 17:16:49 indexcov: 0 principal components, not plotting
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x18 pc=0x8fe719]
goroutine 1 [running]:
github.com/brentp/goleft/indexcov.plotBins(0xc42020e1a0, 0x32, 0x32, 0xc420246e00, 0x32, 0x32, 0x0, 0x0, 0x0, 0x0, ...)
/home/brentp/go/src/github.com/brentp/goleft/indexcov/plot.go:194 +0x5c9
github.com/brentp/goleft/indexcov.writeIndex(0xc4202f4120, 0xc42020e1a0, 0x32, 0x32, 0x0, 0x0, 0x0, 0xc420246e00, 0x32, 0x32, ...)
/home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:697 +0x2b1
github.com/brentp/goleft/indexcov.Main()
/home/brentp/go/src/github.com/brentp/goleft/indexcov/indexcov.go:396 +0x82f
main.main()
/home/brentp/go/src/github.com/brentp/goleft/cmd/goleft/goleft.go:68 +0x17f
from goleft.
These are alignments vs only one chromosome, which may be the problem:
@SQ SN:NC_008463.1 LN:6537648
from goleft.
any chance you could share the bam and reference privately?
from goleft.
actually just the bai and anonymized bam and reference.
see: https://github.com/brentp/goleft/releases/tag/v0.1.10
to get a program to make a minimal bam.
from goleft.
also, from the lines of your error, it looks like you might have an older version of goleft. can you try the latest version?
from goleft.
Pretty sure it's the latest release from march 15
Mar 15 16:17 goleft_linux64*
./goleft_linux64
goleft Version: 0.1.18
covstats : coverage stats across bams by sampling
depth : parallelize calls to samtools in user-defined windows
depthwed : matricize output from depth to n-sites * n-samples
indexcov : quick coverage estimate using only the bam index
indexsplit : create regions of even coverage across bams/crams
samplename : report samplename(s) from a bam's SM tag
from goleft.
can you share a test-case for this?
from goleft.
thanks for the test-case. you can get past this by using --excludepatt ""
since the default is to exclude chromosomes starting with "NC". I have also improved the warning of excluded chromosomes and fixed an associated bug. This will be out in the next release.
from goleft.
Ok, cheers for letting me know
from goleft.
Related Issues (20)
- Differential header stringency depending on file format HOT 4
- goleft depth sliding window analysis HOT 1
- Feature request: New option --exclude for indexsplit HOT 1
- indexcov support for csi indexes HOT 2
- ndexcv: excluding chromosome: NC_031965 because of exclude-pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d HOT 2
- goleft_linux64 covstats error: panic: EOF HOT 7
- coverage of the customized genome HOT 2
- error: bam is required HOT 4
- link to golang typo
- suggestion: zoomable chromosome depth plots in indexcov HOT 1
- indexcov shows stepwise coverage distribution HOT 4
- Feature request: New option --exclude for covstats HOT 2
- Indexcov errors HOT 2
- error on depth, seems to make temp file it can't find
- Negative alnSpan error HOT 2
- No longer possible to build from source or include in a Docker image HOT 2
- Running Indexcov on cram files with different paths HOT 2
- What is the value of the insert size ? HOT 2
- indexcov: usage with long reads ? HOT 1
- Indexcov searching for cram.bai HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from goleft.