Hello,
I am using Minimap2-2.24 (r1122) to get all-vs-all alignments for a set of sequences, e.g.
minimap2 -x ava-ont -f 0.0001 -t 12 -c -X seq.fasta seq.fasta
There are two sequences that should align to each other, but the output PAF does not contain such alignment.
Out of curiosity, I removed the -c option and I do see a mapping between the two sequences:
16 2175 28 2129 + 18 2180 29 2118 1690 2120 0 tp:A:S cm:i:462 s1:i:1674 dv:f:0.0290 rl:i:95
If I only use those two sequences as input (with the -c option), I now see an alignment:
16 2175 19 2175 + 18 2180 21 2180 2039 2206 0 NM:i:167 ms:i:3438 AS:i:3388 nn:i:0 tp:A:S cm:i:512 s1:i:1720 de:f:0.0573 rl:i:0 cg:Z:4M1I58M1I4M1I124M2I47M3I6M3I28M1D5M2D23M2D35M2I109M2D24M2I82M2D18M1D96M2D58M1D14M1I71M1D43M1I17M2I8M1D3M4I15M1D5M1I24M4D3M1D16M1I14M3D5M1I499M2I238M2I26M1I5M1I7M1D5M1I11M1D6M1I1M2I15M1D7M1I22M1D20M1I6M1D5M1I10M1I48M1D3M1D10M4I2M1D24M1I46M1I44M2D8M1I24M16D58M
I think this is a bug.
Thanks,
Ka Ming
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