Pierre Lindenbaum

I don't see any error here. what's the problem. Did you just open a browser at http://localhost:8080/coverage ? PS: I updated the source code a few hours ago.

check you proxy settings...

> I cannot access to the localhost as I am using a different server no, or ask your sys-admin to redirect the localhost elsewhere

ah, yes, it's undocumented. BamStats04 uses the (old) picard API. All those softwares uses a parameter VALIDATION_STRINGENCY . see Standard Options/ VALIDATION_STRINGENCY in http://picard.sourceforge.net/command-line-overview.shtml adding `VALIDATION_STRINGENCY=SILENT` to the command line...

sorry for my late answer, I don't receive my mail from github for an unknow reason...

I don't know the version of your previous version, but I've added a set of standard filters to remove /ignore some reads: http://lindenb.github.io/jvarkit/BamStats04.html see option "`--filter`" ` mapqlt(1) || MapQUnavailable()...

In fact, it means that a SAMrecord (chrom:start-end) overlaps two regions in your bed > the program doesn't know which bed record, it should use. I don't use this program...

5primemost 3primemost is 'difficult' to implement if a bed region overlap a whole read. As a temporary(?) solution I created the option '-largest' which choose the BED record having the...

@newatil it looks like a probleme with your web proxy. It's unrelated to jvarkit. As your sysadmin/ see https://stackoverflow.com/a/22666646/58082

I've added an option ``` -pr,--programId add a program ID to the clipped SAM records. default: false ``` all the clipped bam should have a new attribute PG.