I am using AMOS tools to convert velvet_asm.afg to SAM:
bank-transact -m velvet_asm.afg -b myBankDir -c
bank2contig -s myBankDir > foo.sam
Surprisingly, some lines in the foo.sam have negative start positions, which violate the SAM format.
Has anyone seen this problem?
These negative positions appear to originate from the velvet_asm.afg. If I am not doing anything wrong, I suggest that bank2contig can use soft clipping to not produce negative start positions. For example: a read with start=-13 and CIGAR=35M can be represented as start=1 and CIGAR=14S21M.
bank-transact -m velvet_asm.afg -b myBankDir -c
bank2contig -s myBankDir > foo.sam
Surprisingly, some lines in the foo.sam have negative start positions, which violate the SAM format.
Has anyone seen this problem?
These negative positions appear to originate from the velvet_asm.afg. If I am not doing anything wrong, I suggest that bank2contig can use soft clipping to not produce negative start positions. For example: a read with start=-13 and CIGAR=35M can be represented as start=1 and CIGAR=14S21M.