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Empty piece in scfmap file leads to further crash in combineConsensus.sh #236

Closed Dmitry-Antipov closed 3 months ago

Dmitry-Antipov commented 3 months ago

path haplotype2_from_utig4-282 <utig4-663<utig4-502[N7310N:tangle]<utig4-327[N101656N:tangle]utig4-282 HAPLOTYPE2 is represented as

path haplotype2-0000168 haplotype2_from_utig4-282 [N11941N] [N7310N] [N7259N] [N101656N] piece000018 end

in scfmap file. All pieces except latest are really small, so it is possible. However combineConsensus does not expect such format with interlacing [NsmthN] and fails with ERROR:piece missing from gapped contig haplotype2-0000168

Dmitry-Antipov commented 3 months ago

Fixed with b47102c236b3e228d400b2a67994b72677def9a9