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Search: Posts Made By: lindenb
Forum: Bioinformatics 06-07-2018, 05:19 AM
Replies: 4
Views: 1,089
Posted By lindenb
> How can I get the read name too ? ......

> How can I get the read name too ?

... printl(R.getReadName()+" "+R.getAttribute("XS")
Forum: Bioinformatics 06-04-2018, 06:51 AM
Replies: 4
Views: 1,089
Posted By lindenb
using bioalcidaejdk:...

using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html


java -jar dist/bioalcidaejdk.jar -e 'stream().forEach(R->println(R.getAttribute("XS")));' in.bam
Forum: Bioinformatics 11-24-2017, 09:35 AM
Replies: 1
Views: 945
Posted By lindenb
cross posted...

cross posted https://stackoverflow.com/questions/47473631
Forum: Bioinformatics 11-08-2017, 05:24 AM
Replies: 1
Views: 1,056
Posted By lindenb
cross posted: https://www.biostars.org/p/282369/

cross posted: https://www.biostars.org/p/282369/
Forum: Bioinformatics 10-26-2017, 07:26 AM
Replies: 1
Views: 2,126
Posted By lindenb
cross posted: https://www.biostars.org/p/279970/

cross posted: https://www.biostars.org/p/279970/
Forum: Bioinformatics 07-05-2017, 08:43 AM
Replies: 1
Views: 1,063
Posted By lindenb
cross posted https://www.biostars.org/p/261007/

cross posted https://www.biostars.org/p/261007/
Forum: Bioinformatics 10-05-2016, 09:59 AM
Replies: 3
Views: 1,144
Posted By lindenb
use awk: awk '/^>/ {print;next;}...

use awk:

awk '/^>/ {print;next;} {for(i=0;i<NF;++i) printf("%c",33+int($i));printf("\n");}'

I don't know your endoding. I just put +33. However, your example is strange, if a quality starts...
Forum: Bioinformatics 10-05-2016, 04:56 AM
Replies: 4
Views: 4,647
Posted By lindenb
cross posted https://www.biostars.org/p/215053/

cross posted https://www.biostars.org/p/215053/
Forum: Bioinformatics 07-13-2016, 10:30 AM
Replies: 1
Views: 1,071
Posted By lindenb
cross posted https://www.biostars.org/p/201555/

cross posted https://www.biostars.org/p/201555/
Forum: Bioinformatics 05-12-2016, 02:30 AM
Replies: 1
Views: 1,915
Posted By lindenb
cross posted: https://www.biostars.org/p/191321/

cross posted: https://www.biostars.org/p/191321/
Forum: Bioinformatics 04-19-2016, 03:24 AM
Replies: 3
Views: 1,482
Posted By lindenb
cross posted : https://www.biostars.org/p/187446/

cross posted : https://www.biostars.org/p/187446/
Forum: Bioinformatics 04-18-2016, 09:34 AM
Replies: 1
Views: 952
Posted By lindenb
GATK...

GATK https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php with filterExpression

or

picard FilterVcf with javascript expression.
Forum: Bioinformatics 04-14-2016, 01:36 PM
Replies: 2
Views: 1,171
Posted By lindenb
cross posted https://www.biostars.org/p/186797/

cross posted https://www.biostars.org/p/186797/
Forum: Bioinformatics 04-14-2016, 01:31 PM
Replies: 1
Views: 1,041
Posted By lindenb
cross posted: https://www.biostars.org/p/186798/

cross posted: https://www.biostars.org/p/186798/
Forum: Bioinformatics 03-22-2016, 03:33 AM
Replies: 1
Views: 1,305
Posted By lindenb
cross posted https://www.biostars.org/p/182624/

cross posted https://www.biostars.org/p/182624/
Forum: Bioinformatics 02-24-2016, 04:14 AM
Replies: 1
Views: 957
Posted By lindenb
cross posted (and solved):...

cross posted (and solved): https://www.biostars.org/p/178425/
Forum: Bioinformatics 01-10-2016, 01:57 PM
Replies: 2
Views: 1,272
Posted By lindenb
see https://www.biostars.org/p/15992/ ;...

see https://www.biostars.org/p/15992/ ; https://www.biostars.org/p/59340/ ;
Forum: Bioinformatics 01-06-2016, 05:34 AM
Replies: 2
Views: 2,735
Posted By lindenb
there is currently no automatic method to parse...

there is currently no automatic method to parse the ouptut of VEP. you need to find the description of the INFO field for VEP from the...
Forum: Bioinformatics 01-05-2016, 09:55 AM
Replies: 6
Views: 4,682
Posted By lindenb
you need to install java 1.8 : ...

you need to install java 1.8 :

https://github.com/samtools/htsjdk " Java 8 is now required."

and set JAVA_HOME if needed.
Forum: Bioinformatics 01-05-2016, 09:42 AM
Replies: 6
Views: 4,682
Posted By lindenb
as it is said: "see the compiler error output for...

as it is said: "see the compiler error output for details.".
So, what's the compiler output ?
Forum: Bioinformatics 01-05-2016, 09:21 AM
Replies: 6
Views: 4,682
Posted By lindenb
https://github.com/samtools/htsjdk

https://github.com/samtools/htsjdk

example:

import htsjdk.variant.vcf.*;
import htsjdk.variant.variantcontext.*;
import htsjdk.tribble.readers.*;
public class MinVcf
{
public static void...
Forum: Bioinformatics 01-01-2016, 01:28 PM
Replies: 4
Views: 1,917
Posted By lindenb
cross posted: https://www.biostars.org/p/171195/

cross posted: https://www.biostars.org/p/171195/
Forum: Bioinformatics 12-28-2015, 08:32 PM
Replies: 2
Views: 1,693
Posted By lindenb
cross posted: https://www.biostars.org/p/170836/

cross posted: https://www.biostars.org/p/170836/
Forum: Bioinformatics 12-03-2015, 03:20 AM
Replies: 3
Views: 1,423
Posted By lindenb
I don't think you need a sysadmin ,just download...

I don't think you need a sysadmin ,just download ant from http://ant.apache.org/bindownload.cgi and add the executable to your PATH.

Running this for a SAM file would be easy but I just wonder...
Forum: Bioinformatics 12-03-2015, 02:16 AM
Replies: 3
Views: 1,423
Posted By lindenb
I wrote a genomic digester , see...

I wrote a genomic digester , see https://www.biostars.org/p/86480/#86535

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr3.fa.gz" |\
gunzip -c |\
java -jar...
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