fix cstring error

Author: hdashnow

src/strpkg/call.nim

@@ -87,7 +87,7 @@ proc call_main*() =
     if not fileExists(args.bounds):
       quit "couldn't open bounds file"
 
-  if not open(ibam_dist, args.bam, fai=args.fasta, threads=0):
+  if not open(ibam_dist, cstring(args.bam), fai=cstring(args.fasta), threads=0):
     quit "couldn't open bam"
 
   var cram_opts = 8191 - SAM_RNAME.int - SAM_RGAUX.int - SAM_QUAL.int - SAM_SEQ.int
@@ -103,7 +103,7 @@ proc call_main*() =
   ibam_dist.close()
   ibam_dist = nil
   var ibam:Bam
-  if not open(ibam, args.bam, fai=args.fasta, threads=0, index=true):
+  if not open(ibam, cstring(args.bam), fai=cstring(args.fasta), threads=0, index=true):
     quit "couldn't open bam"
   cram_opts = 8191 - SAM_RGAUX.int - SAM_QUAL.int
   discard ibam.set_option(FormatOption.CRAM_OPT_REQUIRED_FIELDS, cram_opts)

src/strpkg/extract.nim

@@ -272,7 +272,7 @@ proc extract_main*() =
   var min_mapq = uint8(parseInt(args.min_mapq))
   var skip_reads = 100000
 
-  if not open(ibam, args.bam, fai=args.fasta, threads=0):
+  if not open(ibam, cstring(args.bam), fai=cstring(args.fasta), threads=0):
     quit "couldn't open bam"
 
   var cram_opts = 8191 - SAM_RNAME.int - SAM_RGAUX.int - SAM_QUAL.int - SAM_SEQ.int
@@ -286,7 +286,7 @@ proc extract_main*() =
     stderr.write_line "10th, 90th percentile of fragment length:", $frag_dist.median(0.1), " ", $frag_dist.median(0.9)
 
   ibam.close()
-  if not open(ibam, args.bam, fai=args.fasta, threads=0, index=true):
+  if not open(ibam, cstring(args.bam), fai=cstring(args.fasta), threads=0, index=true):
     quit "couldn't open bam"
   cram_opts = 8191 - SAM_RGAUX.int - SAM_QUAL.int
   discard ibam.set_option(FormatOption.CRAM_OPT_REQUIRED_FIELDS, cram_opts)

src/strpkg/extract_region.nim

@@ -37,7 +37,7 @@ proc extract_region_main*() =
     quit 0
 
   var ibam:Bam
-  if not ibam.open(opts.bam, fai=opts.fasta, threads=3, index=true):
+  if not ibam.open(cstring(opts.bam), fai=cstring(opts.fasta), threads=3, index=true):
     quit "could not open bam"
 
   var records = newSeq[Record]()
@@ -69,7 +69,7 @@ proc extract_region_main*() =
 
   var obam:Bam
 
-  if not obam.open(opts.output_bam, mode="wb", threads=2):
+  if not obam.open(cstring(opts.output_bam), mode="wb", threads=2):
     quit "couldn't open output bam"
 
   obam.write_header(ibam.hdr)