Open mmokrejs opened 6 years ago
Hi German, please improve the error message and print out the wrong readname.
bamsort SO=coordinate inputthreads=10 outputthreads=10 level=9 index=1 O=foo.refsorted.bam I=foo.bam [V] Reading alignments from source. Invalid alignment: Query name contains illegal symbols /apps/gentoo/usr/lib64/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x68)[0x2aaaab59ef30] bamsort(libmaus2::exception::LibMausException::LibMausException()+0x2b)[0x2aaaaab22dcb] bamsort(+0x1c8eac)[0x2aaaaac73eac] bamsort(+0x1c80a1)[0x2aaaaac730a1] bamsort(+0x9c60f)[0x2aaaaab4760f] bamsort(+0x71bb4)[0x2aaaaab1cbb4] bamsort(+0x754fa)[0x2aaaaab204fa] /apps/gentoo/lib64/libc.so.6(__libc_start_main+0xea)[0x2aaaad08c4fa] bamsort(+0x6c96a)[0x2aaaaab1796a]
samtools-1.5 sort did not report any issues.
samtools-1.5 sort
Hi German, please improve the error message and print out the wrong readname.
samtools-1.5 sort
did not report any issues.