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