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This repository was archived by the owner on Dec 13, 2017. It is now read-only.
Can you correct output definition in README (columns 10-12)?
README says: 'The output is TAB-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end, the number of matching bases, the number of co-linear minimizers in the match and the fraction of matching bases.'
while man:
OUTPUT FORMAT
Minimap outputs mapping positions in the Pairwise mApping Format (PAF). PAF is a TAB-delimited text format with each line con‐sisting of at least 12 fields as are described in the following table:
┌────┬────────┬─────────────────────────────────────────────────────────────┐
│Col │ Type │ Description │
├────┼────────┼─────────────────────────────────────────────────────────────┤
│ 1 │ string │ Query sequence name │
│ 2 │ int │ Query sequence length │
│ 3 │ int │ Query start coordinate (0-based) │
│ 4 │ int │ Query end coordinate (0-based) │
│ 5 │ char │ `+' if query and target on the same strand; `-'if opposite │ │ 6 │ string │ Target sequence name │ │ 7 │ int │ Target sequence length │ │ 8 │ int │ Target start coordinate on the original strand │ │ 9 │ int │ Target end coordinate on the original strand │ │ 10 │ int │ Number of matching bases in the mapping │ │ 11 │ int │ Number bases, including gaps, in the mapping │ │ 12 │ int │ Mapping quality (0-255 with 255 for missing) │ └────┴────────┴─────────────────────────────────────────────────────────────┘
Can you correct output definition in README (columns 10-12)?
README says: 'The output is TAB-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end, the number of matching bases, the number of co-linear minimizers in the match and the fraction of matching bases.'
while man:
OUTPUT FORMAT Minimap outputs mapping positions in the Pairwise mApping Format (PAF). PAF is a TAB-delimited text format with each line con‐sisting of at least 12 fields as are described in the following table: ┌────┬────────┬─────────────────────────────────────────────────────────────┐ │Col │ Type │ Description │ ├────┼────────┼─────────────────────────────────────────────────────────────┤ │ 1 │ string │ Query sequence name │ │ 2 │ int │ Query sequence length │ │ 3 │ int │ Query start coordinate (0-based) │ │ 4 │ int │ Query end coordinate (0-based) │ │ 5 │ char │ `+' if query and target on the same strand; `-' if opposite │ │ 6 │ string │ Target sequence name │ │ 7 │ int │ Target sequence length │ │ 8 │ int │ Target start coordinate on the original strand │ │ 9 │ int │ Target end coordinate on the original strand │ │ 10 │ int │ Number of matching bases in the mapping │ │ 11 │ int │ Number bases, including gaps, in the mapping │ │ 12 │ int │ Mapping quality (0-255 with 255 for missing) │ └────┴────────┴─────────────────────────────────────────────────────────────┘