include seqpos

dellytools · Oct 23, 2024 · c070639 · c070639
1 parent 9a7dea7
commit c070639
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/R/rd.R b/R/rd.R
@@ -5,7 +5,9 @@ library(gtable)
 library(grid)
 
 chrNamesLong = c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20", "chr21", "chr22", "chrX")
+chrNamesLong = c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20", "chr21", "chr22", "chrX", "chrY")
 chrNamesShort = c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X")
+chrNamesShort = c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y")
 
 # Params
 minCN = 0

diff --git a/src/junction.h b/src/junction.h
@@ -620,7 +620,7 @@ namespace torali
   inline void
   outputSRBamRecords(TConfig const& c, std::vector<std::vector<SRBamRecord> > const& br, bool const longread) {
     // Header
-    std::cerr << "qname\tid\tchr1\tpos1\tchr2\tpos2\tsvtype\tct\tqual\tinslen" << std::endl;
+    std::cerr << "qname\tid\tchr1\tpos1\tchr2\tpos2\tsvtype\tct\tqual\tseqpos\tinslen" << std::endl;
 
     // Hash reads
     typedef std::map<std::size_t, std::string> THashMap;
@@ -660,7 +660,7 @@ namespace torali
     // SVs
     for(uint32_t svt = 0; svt < br.size(); ++svt) {
       for(uint32_t i = 0; i < br[svt].size(); ++i) {
-	std::cerr << hm[br[svt][i].id] << '\t' << br[svt][i].id << '\t' << hdr->target_name[br[svt][i].chr] << '\t' << br[svt][i].pos << '\t' << hdr->target_name[br[svt][i].chr2] << '\t' << br[svt][i].pos2 << '\t' << _addID(svt) << '\t' << _addOrientation(svt) << '\t' << br[svt][i].qual << '\t' << br[svt][i].inslen << std::endl;
+	std::cerr << hm[br[svt][i].id] << '\t' << br[svt][i].id << '\t' << hdr->target_name[br[svt][i].chr] << '\t' << br[svt][i].pos << '\t' << hdr->target_name[br[svt][i].chr2] << '\t' << br[svt][i].pos2 << '\t' << _addID(svt) << '\t' << _addOrientation(svt) << '\t' << br[svt][i].qual << '\t' << br[svt][i].sstart << '\t' << br[svt][i].inslen << std::endl;
       }
     }