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.