Pierre Lindenbaum

@chadisaad ( later ) forget about it, the current code is till buggy, i need to work on this

Ok, I've rewrittern some things https://github.com/lindenb/jvarkit/commit/50c95549a1a68ee34a9c9d168723172febd90cd2 . Can you please test this ?

can you please send those problematic lines in attachment, I cannot copy+paste them without an error. Thanks.

thanks. Works here after https://github.com/lindenb/jvarkit/commit/0efc15763059f91d61141473affa79fd04de8aba ``` [$ java -jar dist/pcrclipreads.jar -B input.bed bug.sam | samtools view -S -out.bam - [INFO][PcrClipReads]reading bed File jeter.bed [INFO][SAMSequenceDictionaryProgress]done: N=3 ``` Can you try again...

You're right thanks, I've recently changed the code but I didnt' test it. I've updated the sources, can you tell me if it works now ? Thanks P.

@srynobio no

Hi again, I got the same problem (?) following https://github.com/brentp/smoove/issues/135 (small CRAM files) ``` [smoove] 2020/11/12 16:17:02 excluding variants with all unknown or homozygous reference genotypes [smoove] 2020/11/12 16:17:02 (..)...

ah ok, sorry, it must be that error: https://github.com/brentp/smoove/issues/91#issuecomment-545585184

@daviesrob thanks for the suggestions, I'll have a look at this in the next days.

I had the time to look back at this. I added a test to test the flags for `BAM_FUNMAP|BAM_FSECONDARY|BAM_FSUPPLEMENTARY|BAM_FQCFAIL|BAM_FDUP` , I updated the expected output files for tests and I...