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comparison rDiff/src/tools/read_utils/remove_reads_from_other_genes.m @ 0:0f80a5141704

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version 0.3 uploaded
author vipints
date Thu, 14 Feb 2013 23:38:36 -0500
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-1:000000000000 0:0f80a5141704
1 function [READS_OUT,FLAG]=remove_reads_from_other_genes(READS,GENE,OFFSET)
2 if nargin==2
3 OFFSET=0;
4 end
5 %This funtion removes the reads in READS which could ome from other
6 %annotated genes. FLAG is 1 if this was sucsesfull and 0 otherwise
7 READS_IN=READS;
8 if isfield(GENE,'non_unique_regions')
9 EXONS=GENE.non_unique_regions;
10 IDX=zeros(1,size(READS,2));
11
12 for i=1:size(EXONS,1)
13 START=max(EXONS(i,1),GENE.start-OFFSET)-GENE.start+1+OFFSET;
14 STOP=min(EXONS(i,2),GENE.stop+OFFSET)-GENE.start+1+OFFSET;
15 IDX(START:STOP)=1;
16 end
17 READS=READS(not(sum(READS(:,IDX>0),2)==sum(READS,2)),:);
18 FLAG=1;
19 READS_OUT=READS;
20 else
21 READS_OUT=READS_IN;
22 FLAG=0;
23 end
24