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