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Trying to fix genomestrip/ ComputeInsertSizeHistogramsWalker "Cannot determine library identifier"

lindenblindenb FranceMember
edited July 2016 in GenomeSTRiP

Hi,
I'm currently trying to analyse a bunch of WGS data that have been generated without the LB tag in the read group. The best thing would be to submit a pull request on the genomestrip code but as far as I know, the code is not available (?).

As a workaround : I've created a patch for htsjdk/samtools/SAMReadGroupRecord.java that will return the sample-name if the library is not available.

public String getLibrary() { final String s= getAttribute(LIBRARY_TAG); return s==null?getSample():s; }

https://gist.github.com/lindenb/580c675e52d47fc043fb4c265337701d

I've replaced the old htsjdk library/jar with the new one.

Q: The old library was named htsjdk-2.1.0.gs. What is that "gs" ? is there any difference with the official htsjdk 2.1.0 release ?. yes, may be ?

Commit message says "fix a bug in htsjdk-2.1.0 preventing multiple ALT headers from being added through the API".

for now , it seems to work so far.

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