* vcfutils.pl: fixed a typo in help message

[samtools.git] / kaln.c

diff --git a/kaln.c b/kaln.c
index 9fe7d6f6cdec9e6f7a5f66197b02ba0c636ec19f..331fbb0aba6b803f4163e6d1acec46a31f6ec99d 100644 (file)
--- a/kaln.c
+++ b/kaln.c
@@ -392,9 +392,19 @@ ka_probpar_t ka_probpar_def = { 0.001, 0.1, 10 };
                 \      \/        \/      \/      /
                  \     /\        /\      /\     /
                        -> D[k-1] -> D[k] ->
-                          \/        \/
 
    M[0] points to every {M,I}[k] and every {M,I}[k] points M[L+1].
+
+   On input, _ref is the reference sequence and _query is the query
+   sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an
+   ambiguous residue. iqual is the base quality. c sets the gap open
+   probability, gap extension probability and band width.
+
+   On output, state and q are arrays of length l_query. The higher 30
+   bits give the reference position the query base is matched to and the
+   lower two bits can be 0 (an alignment match) or 1 (an
+   insertion). q[i] gives the phred scaled posterior probability of
+   state[i] being wrong.
  */
 int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
                                   const ka_probpar_t *c, int *state, uint8_t *q)