Bug in extended CIGAR output

[isovic]

Hi Heng,
Minimap2 is an amazing tool.
There is an edge case I ran into with the extended CIGAR mode, and wanted to report it.
Data for reproducibility can be found in the attachment: test-data-for-minimap2.tar.gz

Concretely, running the following produces output as expected:

$ minimap2 -c ref.fasta query.fasta
query   10111   0   10111   +   ref 10110   4   10110   10105   10112   60  NM:i:7  ms:i:20168  AS:i:20160  nn:i:0  tp:A:P  cm:i:1911   s1:i:10057  s2:i:0  dv:f:0.0004 cg:Z:509M1I4550M1I1878M1D11M1I2652M1I491M1I7M1I7M

When the --eqx flag is used, the output becomes:

$ minimap2 -c --eqx ref.fasta query.fasta
query   10111   0   10111   +   ref 10110   4   10110   10105   10112   60  NM:i:7  ms:i:20168  AS:i:20160  nn:i:0  tp:A:P  cm:i:1911   s1:i:10057  s2:i:0  dv:f:0.0004 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However, the edit distance is still NM:i:7.
Specifying either a larger kmer size, or a smaller window size produces sane alignments again:

$ minimap2 -c --eqx -k 20 ref.fasta query.fasta
query   10111   0   10111   +   ref 10110   4   10110   10105   10112   60  NM:i:7  ms:i:20168  AS:i:20168  nn:i:0  tp:A:P  cm:i:1805   s1:i:10062  s2:i:40 dv:f:0.0004 cg:Z:509=1I4550=1I1878=1D11=1I2652=1I491=1I7=1I7=

$ minimap2 -c --eqx -w 5 ref.fasta query.fasta
query   10111   0   10111   +   ref 10110   4   10110   10105   10112   60  NM:i:7  ms:i:20168  AS:i:20168  nn:i:0  tp:A:P  cm:i:3440   s1:i:10074  s2:i:0  dv:f:0.0004 cg:Z:509=1I4550=1I1878=1D11=1I2652=1I491=1I7=1I7=

I tested it on v2.13 and v2.14, and the results are the same.

Hope this helps,
Best regards,
Ivan.

[lh3]

Thanks so much for the exact example! Very informative.

[isovic]

No problem, any time.
Thanks for fixing it so fast!