Commit b8d3581f authored by nchernia's avatar nchernia
Browse files

fixing assumption of two reads for duplicate marking

parent d824d725

CPU/common/dups_sam.awk

+12 −12
Changes for CPU/common/dups_sam.awk: 12 added lines, 12 removed lines.
Original line number Diff line number Diff line
@@ -136,14 +136,14 @@ $0 !~ /^@/ && $0 ~ /cb:/ && pname != $1 { 
	    for (j=0; j<i; j++) {

		if (j in dups) {

		    count_dups++;

		    markduplicate(saved1[rname[j]]);

		    markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved1) markduplicate(saved1[rname[j]]);

		    if (rname[j] in saved2) markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved3) markduplicate(saved3[rname[j]]);

		    if (rname[j] in saved4) markduplicate(saved4[rname[j]]);

		}

		else {

		    print saved1[rname[j]];

		    print saved2[rname[j]];

		  if (rname[j] in saved1) print saved1[rname[j]];

		  if (rname[j] in saved2) print saved2[rname[j]];

		  if (rname[j] in saved3) print saved3[rname[j]];

		  if (rname[j] in saved4) print saved4[rname[j]];

		}
@@ -155,8 +155,8 @@ $0 !~ /^@/ && $0 ~ /cb:/ && pname != $1 { 
	}

	# size of potential duplicate array is 1, by definition not a duplicate

	else if (i==1) {

	    print saved1[rname[0]];

	    print saved2[rname[0]];

	    if (rname[0] in saved1) print saved1[rname[0]];

	    if (rname[0] in saved2) print saved2[rname[0]];

	    if (rname[0] in saved3) print saved3[rname[0]];

	    if (rname[0] in saved4) print saved4[rname[0]];

	    delete saved1[rname[0]];
@@ -226,14 +226,14 @@ END { 
	    for (j=0; j<i; j++) {

		if (j in dups) {

		    count_dups++;

		    markduplicate(saved1[rname[j]]);

		    markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved1) markduplicate(saved1[rname[j]]);

		    if (rname[j] in saved2) markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved3) markduplicate(saved3[rname[j]]);

		    if (rname[j] in saved4) markduplicate(saved4[rname[j]]);

		}

		else {

		    print saved1[rname[j]];

		    print saved2[rname[j]];

		    if (rname[j] in saved1) print saved1[rname[j]];

		    if (rname[j] in saved2) print saved2[rname[j]];

		    if (rname[j] in saved3) print saved3[rname[j]];

		    if (rname[j] in saved4) print saved4[rname[j]];

		}
@@ -241,8 +241,8 @@ END { 
	}

	# size of potential duplicate array is 1, by definition not a duplicate

	else if (i==1) {

	    print saved1[rname[0]];

	    print saved2[rname[0]];

	    if (rname[0] in saved1) print saved1[rname[0]];

	    if (rname[0] in saved2) print saved2[rname[0]];

	    if (rname[0] in saved3) print saved3[rname[0]];

	    if (rname[0] in saved4) print saved4[rname[0]];

	}

SLURM/scripts/dups_sam.awk

+12 −12
Changes for SLURM/scripts/dups_sam.awk: 12 added lines, 12 removed lines.
Original line number Diff line number Diff line
@@ -136,14 +136,14 @@ $0 !~ /^@/ && $0 ~ /cb:/ && pname != $1 { 
	    for (j=0; j<i; j++) {

		if (j in dups) {

		    count_dups++;

		    markduplicate(saved1[rname[j]]);

		    markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved1) markduplicate(saved1[rname[j]]);

		    if (rname[j] in saved2) markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved3) markduplicate(saved3[rname[j]]);

		    if (rname[j] in saved4) markduplicate(saved4[rname[j]]);

		}

		else {

		    print saved1[rname[j]];

		    print saved2[rname[j]];

		  if (rname[j] in saved1) print saved1[rname[j]];

		  if (rname[j] in saved2) print saved2[rname[j]];

		  if (rname[j] in saved3) print saved3[rname[j]];

		  if (rname[j] in saved4) print saved4[rname[j]];

		}
@@ -155,8 +155,8 @@ $0 !~ /^@/ && $0 ~ /cb:/ && pname != $1 { 
	}

	# size of potential duplicate array is 1, by definition not a duplicate

	else if (i==1) {

	    print saved1[rname[0]];

	    print saved2[rname[0]];

	    if (rname[0] in saved1) print saved1[rname[0]];

	    if (rname[0] in saved2) print saved2[rname[0]];

	    if (rname[0] in saved3) print saved3[rname[0]];

	    if (rname[0] in saved4) print saved4[rname[0]];

	    delete saved1[rname[0]];
@@ -226,14 +226,14 @@ END { 
	    for (j=0; j<i; j++) {

		if (j in dups) {

		    count_dups++;

		    markduplicate(saved1[rname[j]]);

		    markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved1) markduplicate(saved1[rname[j]]);

		    if (rname[j] in saved2) markduplicate(saved2[rname[j]]);

		    if (rname[j] in saved3) markduplicate(saved3[rname[j]]);

		    if (rname[j] in saved4) markduplicate(saved4[rname[j]]);

		}

		else {

		    print saved1[rname[j]];

		    print saved2[rname[j]];

		    if (rname[j] in saved1) print saved1[rname[j]];

		    if (rname[j] in saved2) print saved2[rname[j]];

		    if (rname[j] in saved3) print saved3[rname[j]];

		    if (rname[j] in saved4) print saved4[rname[j]];

		}
@@ -241,8 +241,8 @@ END { 
	}

	# size of potential duplicate array is 1, by definition not a duplicate

	else if (i==1) {

	    print saved1[rname[0]];

	    print saved2[rname[0]];

	    if (rname[0] in saved1) print saved1[rname[0]];

	    if (rname[0] in saved2) print saved2[rname[0]];

	    if (rname[0] in saved3) print saved3[rname[0]];

	    if (rname[0] in saved4) print saved4[rname[0]];

	}

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