File: PAF.md

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## PAF: a Pairwise mApping Format

PAF is a text format describing the approximate mapping positions between two
set of sequences. PAF is TAB-delimited with each line consisting of the
following predefined fields:

|Col|Type  |Description                               |
|--:|:----:|:-----------------------------------------|
|1  |string|Query sequence name                       |
|2  |int   |Query sequence length                     |
|3  |int   |Query start (0-based)                     |
|4  |int   |Query end (0-based)                       |
|5  |char  |Relative strand: "+" or "-"               |
|6  |string|Target sequence name                      |
|7  |int   |Target sequence length                    |
|8  |int   |Target start on original strand (0-based) |
|9  |int   |Target end on original strand (0-based)   |
|10 |int   |Number of residue matches                 |
|11 |int   |Alignment block length                    |
|12 |int   |Mapping quality (0-255; 255 for missing)  |

If PAF is generated from an alignment, column 10 equals the number of sequence
matches, and column 11 equals the total number of sequence matches, mismatches,
insertions and deletions in the alignment. If alignment is not available,
column 10 and 11 are still required but may be highly inaccurate.

A PAF file may optionally contain SAM-like typed key-value pairs at the end of
each line.