bugfix needed to output column headers for Chimeric.out.junction file
@@ -10,33 +10,6 @@ void ParametersChimeric::initialize(Parameters *pPin)
pP=pPin;
- if (out.junctions) {
- pP->inOut->outChimJunction.open((pP->outFileNamePrefix + "Chimeric.out.junction").c_str());
-
- if (multimapNmax>0)
- pP->inOut->outChimJunction <<
- "chr_donorA" <<"\t"<<
- "brkpt_donorA" <<"\t"<<
- "strand_donorA" <<"\t"<<
- "chr_acceptorB" <<"\t"<<
- "brkpt_acceptorB" <<"\t"<<
- "strand_acceptorB" <<"\t"<<
- "junction_type" <<"\t"<<
- "repeat_left_lenA" <<"\t"<<
- "repeat_right_lenB" <<"\t"<<
- "read_name" <<"\t"<<
- "start_alnA" <<"\t"<<
- "cigar_alnA" <<"\t"<<
- "start_alnB" <<"\t"<<
- "cigar_alnB" <<"\t"<<
- "num_chim_aln" <<"\t"<<
- "max_poss_aln_score" <<"\t"<<
- "non_chim_aln_score" <<"\t"<<
- "this_chim_aln_score" <<"\t"<<
- "bestall_chim_aln_score" <<"\t"<<
- "PEmerged_bool" <<"\t"<<
- "readgrp" <<"\n";
- };
if (out.samOld) {
pP->inOut->outChimSAM.open((pP->outFileNamePrefix + "Chimeric.out.sam").c_str());
pP->inOut->outChimSAM << pP->samHeader;
@@ -67,6 +40,37 @@ void ParametersChimeric::initialize(Parameters *pPin)
};
};
+ if (out.junctions) {
+ pP->inOut->outChimJunction.open((pP->outFileNamePrefix + "Chimeric.out.junction").c_str());
+
+ if (multimapNmax>0)
+ // column headers for Chimeric.out.junction file
+ pP->inOut->outChimJunction <<
+ "chr_donorA" <<"\t"<<
+ "brkpt_donorA" <<"\t"<<
+ "strand_donorA" <<"\t"<<
+ "chr_acceptorB" <<"\t"<<
+ "brkpt_acceptorB" <<"\t"<<
+ "strand_acceptorB" <<"\t"<<
+ "junction_type" <<"\t"<<
+ "repeat_left_lenA" <<"\t"<<
+ "repeat_right_lenB" <<"\t"<<
+ "read_name" <<"\t"<<
+ "start_alnA" <<"\t"<<
+ "cigar_alnA" <<"\t"<<
+ "start_alnB" <<"\t"<<
+ "cigar_alnB" <<"\t"<<
+ "num_chim_aln" <<"\t"<<
+ "max_poss_aln_score" <<"\t"<<
+ "non_chim_aln_score" <<"\t"<<
+ "this_chim_aln_score" <<"\t"<<
+ "bestall_chim_aln_score" <<"\t"<<
+ "PEmerged_bool" <<"\t"<<
+ "readgrp" <<"\n";
+ };
+
+
+
if (out.bam && !pP->outBAMunsorted && !pP->outBAMcoord) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETERS error: --chimOutType WithinBAM requires BAM output\n";
