Dedupping single end (339420a3) · Commits · Chaos / chaos.juicer

CPU/common/chimeric_sam.awk

+2 −2

Changes for CPU/common/chimeric_sam.awk: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -253,7 +253,7 @@ $0 !~ /^@/{
		pos[j] = 1;
		}
		}
		else if (str[j] == 0 && notprimary[j]==1 && length(singleend)>0) {
		else if (str[j] == 0 && notprimary[j]==256 && length(singleend)>0) {
		# count Ms,Ds,Ns,Xs,=s for sequence length
		seqlength=0;
		currstr=tmp[6];
		@@ -737,7 +737,7 @@ END{
		pos[j] = 1;
		}
		}
		else if (str[j] == 0 && notprimary[j]==1 && length(singleend)>0) {
		else if (str[j] == 0 && notprimary[j]==256 && length(singleend)>0) {
		# count Ms,Ds,Ns,Xs,=s for sequence length
		seqlength=0;
		currstr=tmp[6];