Searched refs:trimmed5 (Results 1 – 11 of 11) sorted by relevance
490 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()620 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()776 ra.trimmed5 = (int)(nchar - ra.patFw.length()); in parse()903 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()937 if(nqual++ >= r.trimmed5) { in parse()950 if(nqual++ >= r.trimmed5) { in parse()1073 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()1193 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()
53 trimmed5 = trimmed3 = 0; in reset()270 int trimmed5; // amount actually trimmed off 5' end member
987 minins = max<int>(0, minins - patsrc_->bufa().trimmed5); in resolveOutstandingInRef()988 maxins = max<int>(0, maxins - patsrc_->bufa().trimmed5); in resolveOutstandingInRef()997 minins = max<int>(0, minins - patsrc_->bufb().trimmed5); in resolveOutstandingInRef()998 maxins = max<int>(0, maxins - patsrc_->bufb().trimmed5); in resolveOutstandingInRef()1906 minins = max<int>(0, minins - patsrc_->bufa().trimmed5); in resolveOutstandingInRef()1907 maxins = max<int>(0, maxins - patsrc_->bufa().trimmed5); in resolveOutstandingInRef()1916 minins = max<int>(0, minins - patsrc_->bufb().trimmed5); in resolveOutstandingInRef()1917 maxins = max<int>(0, maxins - patsrc_->bufb().trimmed5); in resolveOutstandingInRef()
167 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()201 if(++nqual > r.trimmed5) { in parse()
698 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()843 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()994 ra.trimmed5 = (int)(nchar - ra.patFw.length()); in parse()1124 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()1156 if(nqual++ >= r.trimmed5) { in parse()1169 if(nqual++ >= r.trimmed5) { in parse()1491 ra.trimmed5 += 1; in parse()1596 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()1704 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()1864 r.trimmed5 = (int)(nchar - r.patFw.length()); in parse()
49 trimmed5 = trimmed3 = 0; in reset()265 int trimmed5; // amount actually trimmed off 5' end member
1247 r.trimmed5 = r.patFw.length() - pp_.trimTo.second; in trim()1248 r.patFw.trimEnd(r.trimmed5); in trim()1249 r.qual.trimEnd(r.trimmed5); in trim()
573 r.trimmed5 = trimmed5_[cur_];623 ra.trimmed5 = trimmed5_[cur_];628 rb.trimmed5 = trimmed5_[cur_];836 r.trimmed5 = mytrim5;1152 r.trimmed5 = mytrim5;1206 r.trimmed5 = mytrim5;1277 ra.trimmed5 = mytrim5_1;1338 rb.trimmed5 = mytrim5_2;1718 ra.trimmed5 = gTrim5;1724 rb.trimmed5 = gTrim5;
57 trimmed5 = trimmed3 = 0; in reset()357 int trimmed5; // amount actually trimmed off 5' end member
272 r.trimmed5 = mytrim5; in read()
1573 r.trimmed5 = mytrim5; in read()