BRASS filter generation fails with an uninformative error when *.bas not present

[edawson]

I was working through generating a PON and got a strange error when running the brassI_np_in.pl script:

> brassI_np_in.pl `pwd` 1 /dat/redacted.20k.bam
Starting: /opt/wtsi-cgp/bin/bamcollate2 outputformat=sam exclude=PROPER_PAIR,UNMAP,MUNMAP,SECONDARY,QCFAIL,DUP,SUPPLEMENTARY mapqthres=6 classes=F,F2 T=/home/ubuntu/redacted/tmpMap/bamcollate2 filename=/dat/redacted.20k.bam | /usr/bin/perl /opt/wtsi-cgp/bin/brassI_prep_bam.pl -b /dat/redacted.20k.bam.bas -np | /opt/wtsi-cgp/bin/bamsort inputformat=sam verbose=0 index=1 md5=1 tmpfile=/home/ubuntu/redacted/tmpMap/bamsort md5filename=/home/ubuntu/redacted/redacted.brm.bam.md5 indexfilename=/home/ubuntu/redacted/redacted.brm.bam.bai O=/home/ubuntu/redacted/redacted.brm.bam
ScramDecoder::readAlignment(): failed to read alignment without reaching EOF

/opt/wtsi-cgp/bin/../lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x54)[0x7f42b94b2a54]
/opt/wtsi-cgp/bin/bamsort(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x454550]
/opt/wtsi-cgp/bin/bamsort(libmaus2::bambam::ScramDecoder::readAlignmentInternal(bool)+0x2b3)[0x47b7b3]
/opt/wtsi-cgp/bin/bamsort(bamsort(libmaus2::util::ArgInfo const&)+0x2519)[0x44e309]
/opt/wtsi-cgp/bin/bamsort(main+0x177e)[0x44724e]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f42b7da2f45]
/opt/wtsi-cgp/bin/bamsort()[0x44819f]

WARNING: SAM header designates more than one PG tree root by PP tags.
WARNING: PG line with id bwamem.2 has multiple children referencing it by PP tags.
WARNING: PG line with id bwamem.3 has multiple children referencing it by PP tags.
WARNING: PG line with id bwamem.4 has multiple children referencing it by PP tags.
WARNING: PG line with id bwamem.8 has multiple children referencing it by PP tags.

I grabbed the command line invocations from the first line, started running them individually and found that the second command fails because there's no .bas file:

/opt/wtsi-cgp/bin/bamcollate2 outputformat=sam exclude=PROPER_PAIR,UNMAP,MUNMAP,SECONDARY,QCFAIL,DUP,SUPPLEMENTARY mapqthres=6 classes=F,F2 T=/home/ubuntu/redacted/tmpMap/bamcollate2 filename=/dat/redacted.20k.bam | /usr/bin/perl /opt/wtsi-cgp/bin/brassI_prep_bam.pl -b /dat/redacted.20k.bam.bas -np
File not found: /dat/redacted.20k.bam.bas

Creating a .bas file fixes the issue.

Is it possible to propagate the underlying error better?

[sb43]

This is now fixed.