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Search: Posts Made By: lindenb
Forum: Bioinformatics 06-07-2018, 04:19 AM
Replies: 4
Views: 1,052
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, 05:51 AM
Replies: 4
Views: 1,052
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, 08:35 AM
Replies: 1
Views: 918
Posted By lindenb
cross posted...

cross posted https://stackoverflow.com/questions/47473631
Forum: Bioinformatics 11-08-2017, 04:24 AM
Replies: 1
Views: 1,027
Posted By lindenb
cross posted: https://www.biostars.org/p/282369/

cross posted: https://www.biostars.org/p/282369/
Forum: Bioinformatics 10-26-2017, 06:26 AM
Replies: 1
Views: 2,028
Posted By lindenb
cross posted: https://www.biostars.org/p/279970/

cross posted: https://www.biostars.org/p/279970/
Forum: Bioinformatics 07-05-2017, 07:43 AM
Replies: 1
Views: 1,032
Posted By lindenb
cross posted https://www.biostars.org/p/261007/

cross posted https://www.biostars.org/p/261007/
Forum: Bioinformatics 10-05-2016, 08:59 AM
Replies: 3
Views: 1,121
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, 03:56 AM
Replies: 4
Views: 4,449
Posted By lindenb
cross posted https://www.biostars.org/p/215053/

cross posted https://www.biostars.org/p/215053/
Forum: Bioinformatics 07-13-2016, 09:30 AM
Replies: 1
Views: 1,044
Posted By lindenb
cross posted https://www.biostars.org/p/201555/

cross posted https://www.biostars.org/p/201555/
Forum: Bioinformatics 05-12-2016, 01:30 AM
Replies: 1
Views: 1,870
Posted By lindenb
cross posted: https://www.biostars.org/p/191321/

cross posted: https://www.biostars.org/p/191321/
Forum: Bioinformatics 04-19-2016, 02:24 AM
Replies: 3
Views: 1,402
Posted By lindenb
cross posted : https://www.biostars.org/p/187446/

cross posted : https://www.biostars.org/p/187446/
Forum: Bioinformatics 04-18-2016, 08:34 AM
Replies: 1
Views: 911
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, 12:36 PM
Replies: 2
Views: 1,143
Posted By lindenb
cross posted https://www.biostars.org/p/186797/

cross posted https://www.biostars.org/p/186797/
Forum: Bioinformatics 04-14-2016, 12:31 PM
Replies: 1
Views: 1,020
Posted By lindenb
cross posted: https://www.biostars.org/p/186798/

cross posted: https://www.biostars.org/p/186798/
Forum: Bioinformatics 03-22-2016, 02:33 AM
Replies: 1
Views: 1,267
Posted By lindenb
cross posted https://www.biostars.org/p/182624/

cross posted https://www.biostars.org/p/182624/
Forum: Bioinformatics 02-24-2016, 03:14 AM
Replies: 1
Views: 905
Posted By lindenb
cross posted (and solved):...

cross posted (and solved): https://www.biostars.org/p/178425/
Forum: Bioinformatics 01-10-2016, 12:57 PM
Replies: 2
Views: 1,242
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, 04:34 AM
Replies: 2
Views: 2,660
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, 08:55 AM
Replies: 6
Views: 4,548
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, 08:42 AM
Replies: 6
Views: 4,548
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, 08:21 AM
Replies: 6
Views: 4,548
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, 12:28 PM
Replies: 4
Views: 1,852
Posted By lindenb
cross posted: https://www.biostars.org/p/171195/

cross posted: https://www.biostars.org/p/171195/
Forum: Bioinformatics 12-28-2015, 07:32 PM
Replies: 2
Views: 1,650
Posted By lindenb
cross posted: https://www.biostars.org/p/170836/

cross posted: https://www.biostars.org/p/170836/
Forum: Bioinformatics 12-03-2015, 02:20 AM
Replies: 3
Views: 1,388
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, 01:16 AM
Replies: 3
Views: 1,388
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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