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ekg / glia

a string to graph aligner
MIT License
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Fixes for regional BAM re-alignment with bgzipped inputs: glia: out_of_range and tabix errors #1

Open chapmanb opened 10 years ago

chapmanb commented 10 years ago

Eric; This fixes two issues I ran into while using glia for realignment included called variants.

Here's a small reproducible test case that triggers these errors.

wget https://github.com/chapmanb/bcbio.variation.plus/raw/master/test/data/ensemble/NA12878-10.bam
wget https://raw.github.com/chapmanb/bcbio.variation.plus/master/test/data/ensemble/chr10-start.fa
wget https://s3.amazonaws.com/chapmanb/union-10_250000_400000.vcf.gz
tabix -p vcf union-10_250000_400000.vcf.gz
samtools view -bu NA12878-10.bam | glia -d -Rr -w 1000 -S 200 -Q 200 -G 4 -f chr10-start.fa -v union-10_250000_400000.vcf.gz

Thanks again for this tool. I'm excited to have a minimal test case running with it and looking forward to exploring more.

ekg commented 10 years ago

Hi Brad,

In trying to run the test I hit a snag. The BAM file (https://github.com/chapmanb/bcbio.variation.plus/raw/master/test/data/ensemble/NA12878-10.bam) does not appear to exist, or the URL has changed. Could you please update this and I'll run the tests.

chapmanb commented 10 years ago

Erik; Sorry about this. I moved these over to another repository. The new wgets are:

wget https://github.com/chapmanb/bcbio.variation.recall/raw/master/test/data/ensemble/NA12878-10.bam
wget https://raw.github.com/chapmanb/bcbio.variation.recall/master/test/data/ensemble/chr10-start.fa

Please let me know if you run into anything else. Thanks much for looking at these.

ekg commented 10 years ago

Great, I've just downloaded them.

On Fri, Jan 31, 2014 at 7:22 AM, Brad Chapman notifications@github.comwrote:

Erik; Sorry about this. I moved these over to another repository. The new wgets are:

wget https://github.com/chapmanb/bcbio.variation.recall/raw/master/test/data/ensemble/NA12878-10.bam wget https://raw.github.com/chapmanb/bcbio.variation.recall/master/test/data/ensemble/chr10-start.fa

Please let me know if you run into anything else. Thanks much for looking at these.

Reply to this email directly or view it on GitHubhttps://github.com/ekg/glia/pull/1#issuecomment-33789855 .

yifangt commented 7 years ago

I was wondering where the "fastq.h" header is or, it may not be needed?

jollymrt commented 6 years ago

Hi Erik,

I am trying to run glia to realign a bam file around indels but getting the following error "Command not found : glia Did you mean ...." how to resolve this issue. I am currently in glia directory and have run make and cmake on both bam and glia. I dont see any executable or dll files after running make. Can you please help.

Regards Jolly

ekg commented 6 years ago

Glia needs to be in a directory in your PATH environment variable. This is a Unix level issue that you can resolve by putting the executable in an expected place or adding the current directory with it to the path.

I should reiterate, use vg rather than glia. It has had hundreds of times the use and developmental effort.

https://github.com/vgteam/vg

On Fri, Aug 10, 2018, 00:07 jollymrt notifications@github.com wrote:

Hi Erik,

I am trying to run glia to realign a bam file around indels but getting the following error "Command not found : glia Did you mean ...." how to resolve this issue. I am currently in glia directory and have run make and cmake on both bam and glia. I dont see any executable or dll files after running make. Can you please help.

Regards Jolly

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ekg/glia/pull/1#issuecomment-411913589, or mute the thread https://github.com/notifications/unsubscribe-auth/AAI4EYBaeKE2Js46IJUchaartmnwpkvZks5uPLKugaJpZM4BVx3Z .

jollymrt commented 6 years ago

Hi Erik,

Thanks for your response. Basically I need to run a realignment on the bam files that will then be used for our in-house variant caller. I looked up vg but it does not have a separate realignment tool or may be I did not looked up thoroughly. Can you please point if this exists in vg ? Also in glia, I did not see any executable file in the package after running make. Will the file be made in a different folder?

Again thanks for your help.

Regards

On Fri, Aug 10, 2018 at 12:43 AM, Erik Garrison notifications@github.com wrote:

Glia needs to be in a directory in your PATH environment variable. This is a Unix level issue that you can resolve by putting the executable in an expected place or adding the current directory with it to the path.

I should reiterate, use vg rather than glia. It has had hundreds of times the use and developmental effort.

https://github.com/vgteam/vg

On Fri, Aug 10, 2018, 00:07 jollymrt notifications@github.com wrote:

Hi Erik,

I am trying to run glia to realign a bam file around indels but getting the following error "Command not found : glia Did you mean ...." how to resolve this issue. I am currently in glia directory and have run make and cmake on both bam and glia. I dont see any executable or dll files after running make. Can you please help.

Regards Jolly

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ekg/glia/pull/1#issuecomment-411913589, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAI4EYBaeKE2Js46IJUchaartmnwpkvZks5uPLKugaJpZM4BVx3Z .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ekg/glia/pull/1#issuecomment-412003374, or mute the thread https://github.com/notifications/unsubscribe-auth/ACaFZjwHlZdqh2CX1ZExNnsxnQhpP5vzks5uPTmRgaJpZM4BVx3Z .

-- Jolly Shrivastava Ph.D (Genetics, Genomics and Bioinformatics) University of California, Riverside

ekg commented 6 years ago

@jollymrt let's continue this conversation here: https://github.com/vgteam/vg/issues/1823