From e4131ee876bbde70ae164fd768ad177f10836723 Mon Sep 17 00:00:00 2001 From: earonesty Date: Wed, 17 Sep 2014 20:31:45 +0000 Subject: [PATCH] fix 1 more time for RNA seq varall diversity --- clipper/varcall.cpp | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/clipper/varcall.cpp b/clipper/varcall.cpp index 63173c0..fee0bdd 100644 --- a/clipper/varcall.cpp +++ b/clipper/varcall.cpp @@ -1054,6 +1054,9 @@ inline void PileupSummary::Parse(char *line, PileupReads &rds, tidx *adex, char // position of read relative to my position int pia = read_i->Pos >= 0 ? Pos-read_i->Pos : 0; + + pia = pia % (meanreadlen*2); + if (pia >= depthbypos.size()) { depthbypos.resize(pia+1); depthbyposbycall.resize(pia+1); @@ -1077,7 +1080,8 @@ inline void PileupSummary::Parse(char *line, PileupReads &rds, tidx *adex, char is_ref = 1; } - if (o == '>' || o == '<') { + if (o == '>' || o == '<') { + /// splice! don't add to SEQ or depth, etc! c = 'N'; // no call is_ref = 1; } @@ -1177,7 +1181,7 @@ inline void PileupSummary::Parse(char *line, PileupReads &rds, tidx *adex, char if (c == '-' || c == '+') { warn("invalid pileup, at '%s', indel not attached to read?\n", cur_p); } else { - if (c != '*') + if (c != '*' && c != 'N') read_i->Seq += c; ++cur_p; } @@ -1279,9 +1283,6 @@ inline void PileupSummary::Parse(char *line, PileupReads &rds, tidx *adex, char } } - if (max_pia > meanreadlen*2) - max_pia=meanreadlen*2; - // bool quit=0; for (i=0;i < Calls.size();++i) { // total depth (exclude inserts for tot depth, otherwise they are double-counted) if (Calls[i].depth()>0) {