Loading CPU/common/chimeric_sam.awk +41 −6 Changes for CPU/common/chimeric_sam.awk: 41 added lines, 6 removed lines. Original line number Diff line number Diff line Loading @@ -596,7 +596,7 @@ $0 !~ /^@/{ interiorpos1 = adjust(pos[read1],str[read1],cigarstr[read1],notprimary[read1]); interiorpos2 = adjust(pos[read2],str[read2],cigarstr[read2],notprimary[read2]); sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",interiorpos1,interiorpos2); cb_str = "cb:Z:"chr[read1]"_"chr[2]"_"fragstr"_"str[read1]"_"outputstr"_"sortpos; cb_str = "cb:Z:"chr[read1]"_"chr[read2]"_"fragstr"_"str[read1]"_"outputstr"_"sortpos; # assign mate mapping quality, "read type", "interior position", "mate interior position" # unclear for singleend what the read type should be; both 0/1 and 2/3 are possible Loading Loading @@ -643,11 +643,29 @@ $0 !~ /^@/{ split(c[i], tmp); # blacklist - if 3rd bit set (=4) it means unmapped mapped[j] = and(tmp[2],4) == 0; str[j] = and(tmp[2],16); # chromosome chr[j] = tmp[3]; # get rid of "_" in chromosome name, for cb_str gsub(/_/, "", chr[j]); # position pos[j] = tmp[4]; # cigar string cigarstr[j] = tmp[6]; } if (mapped[0]) { if (mapped[0] && length(singleend)>0) { count_singleton++; # get 3' end for second end for dedupping interiorpos1 = adjust(pos[0],str[0],cigarstr[0],0); sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",pos[0],interiorpos1); cb_str = "cb:Z:"chr[0]"_"chr[0]"_0_1_"str[0]"_"str[0]"_"sortpos; # read type 7 is singleton reads print c[1],"rt:A:7",cb_str; } else if (mapped[0]) { count_singleton++; for (i in c) { print c[i],"rt:A:8"; print c[i],"rt:A:7"; } } else { Loading Loading @@ -1106,14 +1124,31 @@ END{ j=0; for (i in c) { split(c[i], tmp); split(tmp[1],readname,"/"); # blacklist - if 3rd bit set (=4) it means unmapped mapped[j] = and(tmp[2],4) == 0; str[j] = and(tmp[2],16); # chromosome chr[j] = tmp[3]; # get rid of "_" in chromosome name, for cb_str gsub(/_/, "", chr[j]); # position pos[j] = tmp[4]; # cigar string cigarstr[j] = tmp[6]; } if (mapped[0]) { if (mapped[0] && length(singleend)>0) { count_singleton++; # get 3' end for second end for dedupping interiorpos1 = adjust(pos[0],str[0],cigarstr[0],0); sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",pos[0],interiorpos1); cb_str = "cb:Z:"chr[0]"_"chr[0]"_0_1_"str[0]"_"str[0]"_"sortpos; # read type 7 is singleton reads print c[1],"rt:A:7",cb_str; } else if (mapped[0]) { count_singleton++; for (i in c) { print c[i],"rt:A:8"; print c[i],"rt:A:7"; } } else { Loading Loading
CPU/common/chimeric_sam.awk +41 −6 Changes for CPU/common/chimeric_sam.awk: 41 added lines, 6 removed lines. Original line number Diff line number Diff line Loading @@ -596,7 +596,7 @@ $0 !~ /^@/{ interiorpos1 = adjust(pos[read1],str[read1],cigarstr[read1],notprimary[read1]); interiorpos2 = adjust(pos[read2],str[read2],cigarstr[read2],notprimary[read2]); sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",interiorpos1,interiorpos2); cb_str = "cb:Z:"chr[read1]"_"chr[2]"_"fragstr"_"str[read1]"_"outputstr"_"sortpos; cb_str = "cb:Z:"chr[read1]"_"chr[read2]"_"fragstr"_"str[read1]"_"outputstr"_"sortpos; # assign mate mapping quality, "read type", "interior position", "mate interior position" # unclear for singleend what the read type should be; both 0/1 and 2/3 are possible Loading Loading @@ -643,11 +643,29 @@ $0 !~ /^@/{ split(c[i], tmp); # blacklist - if 3rd bit set (=4) it means unmapped mapped[j] = and(tmp[2],4) == 0; str[j] = and(tmp[2],16); # chromosome chr[j] = tmp[3]; # get rid of "_" in chromosome name, for cb_str gsub(/_/, "", chr[j]); # position pos[j] = tmp[4]; # cigar string cigarstr[j] = tmp[6]; } if (mapped[0]) { if (mapped[0] && length(singleend)>0) { count_singleton++; # get 3' end for second end for dedupping interiorpos1 = adjust(pos[0],str[0],cigarstr[0],0); sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",pos[0],interiorpos1); cb_str = "cb:Z:"chr[0]"_"chr[0]"_0_1_"str[0]"_"str[0]"_"sortpos; # read type 7 is singleton reads print c[1],"rt:A:7",cb_str; } else if (mapped[0]) { count_singleton++; for (i in c) { print c[i],"rt:A:8"; print c[i],"rt:A:7"; } } else { Loading Loading @@ -1106,14 +1124,31 @@ END{ j=0; for (i in c) { split(c[i], tmp); split(tmp[1],readname,"/"); # blacklist - if 3rd bit set (=4) it means unmapped mapped[j] = and(tmp[2],4) == 0; str[j] = and(tmp[2],16); # chromosome chr[j] = tmp[3]; # get rid of "_" in chromosome name, for cb_str gsub(/_/, "", chr[j]); # position pos[j] = tmp[4]; # cigar string cigarstr[j] = tmp[6]; } if (mapped[0]) { if (mapped[0] && length(singleend)>0) { count_singleton++; # get 3' end for second end for dedupping interiorpos1 = adjust(pos[0],str[0],cigarstr[0],0); sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",pos[0],interiorpos1); cb_str = "cb:Z:"chr[0]"_"chr[0]"_0_1_"str[0]"_"str[0]"_"sortpos; # read type 7 is singleton reads print c[1],"rt:A:7",cb_str; } else if (mapped[0]) { count_singleton++; for (i in c) { print c[i],"rt:A:8"; print c[i],"rt:A:7"; } } else { Loading
