From 6817791840759ae97b63c3690c7e0e21bf514986 Mon Sep 17 00:00:00 2001 From: Simon Ye Date: Tue, 29 Aug 2017 00:27:37 -0400 Subject: [PATCH] Fix cd-hit-dup for mismatches Previously would only cluster perfect matches except for mismatches close to the end (~10 bp) --- cd-hit-auxtools/cdhit-dup.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cd-hit-auxtools/cdhit-dup.cxx b/cd-hit-auxtools/cdhit-dup.cxx index 8a982da..c00606f 100644 --- a/cd-hit-auxtools/cdhit-dup.cxx +++ b/cd-hit-auxtools/cdhit-dup.cxx @@ -369,7 +369,7 @@ void ClusterDuplicate( SequenceList & seqlist, Array & clusters int start = primer; dep = 0;//HashingDepth( shared, min ); - while( maxmm == 0 && clustered == false && (start+2*shared) <= qlen && start <= primer + (maxmm+1) * shared ){ + while( maxmm > 0 && clustered == false && (start+2*shared) <= qlen && start <= primer + (maxmm+1) * shared ){ hash = MakeHash( seq, start, shared ); node = middles[start][ dep ].Find( hash ); start += shared;