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bamsort: Query name contains illegal symbols

Open mmokrejs opened this issue 6 years ago • 0 comments

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.

mmokrejs avatar Apr 13 '18 15:04 mmokrejs