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updated mappy and example.c

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Heng Li
2017-10-16 11:15:07 -04:00
parent adf6cd7f52
commit b24c9c90c7
6 changed files with 28 additions and 15 deletions
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python/README.rst
+7 -3
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@@ -104,9 +104,13 @@ properties:
* **mapq**: mapping quality
* **NM**: number of mismatches and gaps in the alignment
* **blen**: length of the alignment, including both alignment matches and gaps
but excluding ambiguous bases.
* **mlen**: length of the matching bases in the alignment, excluding ambiguous
base matches.
* **NM**: number of mismatches, gaps and ambiguous poistions in the alignment
* **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
reverse strand; 0 if unknown
@@ -124,7 +128,7 @@ the following format:
::
q_st q_en strand ctg ctg_len r_st r_en blen-NM blen mapq cg:Z:cigar_str
q_st q_en strand ctg ctg_len r_st r_en mlen blen mapq cg:Z:cigar_str
It is effectively the PAF format without the QueryName and QueryLength columns
(the first two columns in PAF).