add bulk sample support

src/sscocaller.nim

@@ -76,14 +76,19 @@ proc countAllele(rec:Variant, ibam:Bam, maxTotalReads:int,
   rec_alt = rec.ALT[0][0]
   for aln in ibam.query(chrom = chrom,start = rec.POS.cint-1, stop = rec.POS.cint):
     var cbt = tag[string](aln, "CB")
+    var currentCB: string
     if cbt.isNone:
     #  echo "no cb "
-      continue  
+      if not bulkBam:
+        continue  
+      else:
+        currentCB = "bulk"
+    else:
+      currentCB = cbt.get  
     if aln.flag.unmapped or aln.mapping_quality.cint < mapq or aln.flag.dup: continue
     ## skip unmapped, duplicated, mapq low reads or aln.flag.secondary or aln.flag.supplementary
     ## if not aln.flag.proper_pair: continue
-
-    if not barcodeTable.hasKey(cbt.get): 
+    if not barcodeTable.hasKey(currentCB): 
       continue
     var 
       off = aln.start.int
@@ -110,21 +115,21 @@ proc countAllele(rec:Variant, ibam:Bam, maxTotalReads:int,
     if aln.base_quality_at(qoff - over-1).cint < minbsq: 
       continue
     total_reads+=1
-    if alleleCountTable.hasKey(cbt.get):
+    if alleleCountTable.hasKey(currentCB):
       if aln.base_at(qoff - over-1) == rec.REF[0]: 
-        alleleCountTable[cbt.get].inc_count_cref
+        alleleCountTable[currentCB].inc_count_cref
         continue
       if aln.base_at(qoff - over-1) == rec_alt: 
-        alleleCountTable[cbt.get].inc_count_calt
+        alleleCountTable[currentCB].inc_count_calt
         continue
     else:
       var new_snp = allele_expr(cref:0,calt:0)
-      alleleCountTable[cbt.get] = new_snp
+      alleleCountTable[currentCB] = new_snp
       if aln.base_at(qoff - over-1) == rec.REF[0]: 
-        alleleCountTable[cbt.get].inc_count_cref
+        alleleCountTable[currentCB].inc_count_cref
         continue
       if aln.base_at(qoff - over-1) == rec_alt: 
-        alleleCountTable[cbt.get].inc_count_calt
+        alleleCountTable[currentCB].inc_count_calt
         continue
   if total_reads > maxTotalReads or total_reads < minTotalReads:
     return initTable[string,allele_expr]()
@@ -179,7 +184,6 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
       outFileSNPanno = openFileStream(out_dir & chrom & "_snpAnnot.txt", fmWrite)
       outFileTotalCountMtx = openFileStream(out_dir & chrom & "_totalCount.mtx", fmWrite)
       outFileAltCountMtx = openFileStream(out_dir & chrom & "_altCount.mtx", fmWrite)
-      # outHeaderMtx = openFileStream(out_dir & chrom & "_header.mtx", fmWrite)
       outFileVStateMtx = openFileStream(out_dir & chrom & "_vi.mtx", fmWrite)
       viSegmentInfo = openFileStream(out_dir & chrom & "_viSegInfo.txt", fmWrite)
       #echo strm.readLine()
@@ -217,7 +221,6 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
         # ac.tostring(acs)
         ## mindp, maxdp, they are values per cell
         if (ac.cref+ac.calt) <= mindp or (ac.cref+ac.calt) >= maxdp: continue        
-
         var ithSperm = barcodeTable[bc]
         ## write to mtx Ref count
         outFileTotalCountMtx.writeLine($snpIndex & " " & $(ithSperm+1) & " " & $(ac.cRef+ac.cAlt))