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in trimq() change 1-based to 0-based

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1 parent 39fbc85 commit 7ff74ecfead6935ab7611f3f8249df70c13d9c63 Heng Li committed Jan 17, 2012
Showing with 3 additions and 5 deletions.
  1. +1 −1 addon.c
  2. +2 −4 awk.1
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@@ -213,7 +213,7 @@ Cell *bio_func(int f, Cell *x, Node **a)
if (s > max) max = s, beg = tmp, end = i + 1;
if (s < 0) s = 0, tmp = i + 1;
}
- if (u) { setfval(u, beg + 1); tempfree(u); } /* 1-based position; as substr() is 1-based. */
+ if (u) { setfval(u, beg); tempfree(u); } /* 1-based position; as substr() is 1-based. */
if (v) { setfval(v, end); tempfree(v); }
} else if (f == BIO_FQUALCOUNT) {
if (a[1]->nnext == 0) {
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@@ -561,11 +561,9 @@ in the IUB encoding.
trim quality string
.I qual
in the Sanger scale using Richard Mott's algorithm (used in Phred). The
-beginning and ending positions are written to
+0-based beginning and ending positions are written to
.IR beg " and " end ,
-respectively. The positions are 1-based as in
-.BR substr() .
-The last arguement
+respectively. The last arguement
.I param
is the single parameter used in the algorithm, which is optional and defaults 0.05.
.TP

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