search

lh3 / minimap

This repo is DEPRECATED. Please use minimap2, the successor of minimap.
https://github.com/lh3/minimap2
MIT License
106 stars 29 forks source link

Output format in readme is different from minimap.1 #3

Open lpryszcz opened 8 years ago

lpryszcz commented 8 years ago

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)                │
                                └────┴────────┴─────────────────────────────────────────────────────────────┘