extract_discordants.py deletes the original BAM file

[cjfields]

When running extract_discordants.py on our cluster, I noticed two issues, the first pretty severe. Any ideas?

• When extracting the original (query-ordered) BAM file, a *.bedpe file is generated. However, when running the assembly step in the pipeline, the original BAM files were missing. I decided to copy my position-sorted file over to test this; the BEDPE was again generated, but the BAM file extracted was deleted when finished. Not sure if this is pysam-specific. I luckily had a sorted backup BAM (each file was ~ 50GB), but looks like I have to rerun a query-sort on those.
• The BEDPE name is incorrectly generated; example original BAM files is JHU_926_5.bam, the generated BEDPE is JHU_926_5.ba.bedpe.

[vbaillet]

Has this issue been addressed ? I notice virtually the same thing with my data, with the BAM files being deleted very early upon running assemble-routed-files.sh. Any suggestions ?