add cell barcode option

src/sscocaller.nim

@@ -59,13 +59,13 @@ proc getTrans(pos1:int64,pos2:int64,cmPmb=0.1): float =
 proc countAllele(rec:Variant, ibam:Bam, maxTotalReads:int,
                   minTotalReads:int,
                   chrom:string, mapq: int,
-                  barcodeTable:OrderedTableRef,minbsq:int,bulkBam:bool): Table[string,allele_expr] =
+                  barcodeTable:OrderedTableRef,minbsq:int,bulkBam:bool,barcodeTag:string): Table[string,allele_expr] =
   var alleleCountTable = initTable[string,allele_expr]()
   var rec_alt:char
   var total_reads=0
   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 cbt = tag[string](aln, barcodeTag)
     var currentCB: string
     if cbt.isNone:
     #  echo "no cb "
@@ -127,7 +127,7 @@ proc countAllele(rec:Variant, ibam:Bam, maxTotalReads:int,
 proc sscocaller(threads:int, vcff:string, barcodeFile:string,
                 bamfile:string, out_dir:string, mapq:int, 
                 minbsq:int, mintotal:int, maxtotal:int, mindp:int, maxdp:int, 
-                thetaREF:float, thetaALT:float, cmPmb:float,s_Chrs:seq): int =
+                thetaREF:float, thetaALT:float, cmPmb:float,s_Chrs:seq,barcodeTag:string): int =
 
   var 
     ibam:Bam
@@ -202,7 +202,8 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
                                          minbsq=minbsq,
                                          maxTotalReads = maxtotal,
                                          minTotalReads = mintotal,
-                                         bulkBam = bulkBam)
+                                         bulkBam = bulkBam,
+                                         barcodeTag = barcodeTag)
       if alleleCountTable.len==0: continue
 
       var rec_alt:char
@@ -404,7 +405,7 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
   return 0
 
 when(isMainModule):
-  let version = "0.2.0"
+  let version = "0.2.1"
   var doc = format("""
   $version
 
@@ -424,6 +425,7 @@ Arguments:
 
 Options:
   -t --threads <threads> number of BAM decompression threads [default: 4]
+  -cb --cellbarcode <cellbarcode> the cell barcode tag, by default it is CB
   -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
   -BQ --baseq <baseq>  base quality threshold for a base to be used for counting [default: 13]
   -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
@@ -459,9 +461,12 @@ Options:
     thetaREF:float
     thetaALT:float
     cmPmb:float
+    barcodeTag="CB"
 
   if($args["--threads"] != "nil"):
       threads = parse_int($args["--threads"])
+  if($args["--cellbarcode"] != "nil"):
+      barcodeTag = $args["--barcodeTag"]
   else: threads = 4
   if($args["--minDP"] != "nil"):
       mindp = parse_int($args["--minDP"])
@@ -530,5 +535,5 @@ Options:
   #var args = commandLineParams()
   discard sscocaller(threads, vcff, barcodeFile, bamfile,
                      out_dir, mapq, minbsq, mintotal, 
-                     maxtotal, mindp, maxdp, thetaREF, thetaALT, cmPmb,s_Chrs)
+                     maxtotal, mindp, maxdp, thetaREF, thetaALT, cmPmb,s_Chrs,barcodeTag)