enabled-danger-compilation

Makefile

@@ -3,16 +3,15 @@
 
 BIN=./bin
 SOURCE=./src
+NIM_PATHS= --colors:on --noNimblePath --path:/local/giovanni/bamtocov/nimbledeps/pkgs/hts-0.3.17 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/docopt-0.6.8 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/regex-0.19.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/unicodedb-0.9.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/lapper-0.1.7 
 VERSION := $(shell grep version bamtocov.nimble  | grep  -o "[0-9]\\+\.[0-9]\.[0-9]\\+")
 LIST=$(BIN)/bamtocov $(BIN)/bamtocounts $(BIN)/covtotarget $(BIN)/bamcountrefs $(BIN)/gff2bed $(BIN)/bamtocounts_legacy $(BIN)/bamtarget
 
 $(BIN)/%: $(SOURCE)/%.nim $(SOURCE)/covutils.nim bamtocov.nimble
-	nim c -d:NimblePkgVersion=$(VERSION) -d:release  --opt:speed -d:danger --out:$@ $<
+	nim c  $(NIM_PATHS)  -d:NimblePkgVersion=$(VERSION) -d:release  --opt:speed -d:danger --out:$@ $<
 
 all: $(LIST)
 
-#bin/bamtocov:
-#	nimble build
 
 test: testshpec 
 

bamtocov.nimble

@@ -10,7 +10,7 @@ license       = "MIT"
 requires "hts >= 0.3.1", "docopt >= 0.6.8", "nim >= 1.0.0", "lapper"
 srcDir = "src"
 binDir = "bin"
-bin = @["covtotarget", "bamtocounts", "bamtocov", "bamcountrefs", "gff2bed"]
+bin = @["covtotarget", "bamtocounts", "bamtocov", "bamcountrefs", "gff2bed", "bamtarget"]
 skipDirs = @["tests", "docs"]
 skipFiles = @["example.bam"]
 

nim.cfg

@@ -1,7 +1,7 @@
 # in htslib: cd 
 # nim c -a -d:static -d:release 
 
-
+-d:danger
 -d:release
 --opt:speed
 @if static:

src/bamtarget.nim

@@ -93,12 +93,11 @@ proc main(argv: var seq[string]): int =
   let doc = format("""
   BamTarget $version
 
-  Usage: BamTarget [options] [<Target>]
+  Usage: BamTarget [options] <Target> [<BAM>]
 
 Arguments:                                                                                                                                                 
   <Target>         A target to be parsed (GFF, GTF, BED)
-
-
+  <BAM>            A BAM file linked to the target
 
 Target files:
   -r, --regions <bed>          Target file in BED or GFF3/GTF format (detected with the extension)
@@ -177,13 +176,27 @@ Other options:
     target = bed_to_table($args["<Target>"])
 
   if debug:
-    stderr.writeLine "Target parsed: ", len(target), " regions"
+    stderr.writeLine "Target parsed: ", len(target), " reference sequences"
+
   for t in target.keys():
     if debug:
       echo "# Chromosome:" , t
     for region in target[t]:
       echo region.chrom, "\t", region.start, "\t", region.stop, "\t", region.name
 
+  if fileExists($args["<BAM>"]):
+    if debug:
+      stderr.writeLine "BAM file: ", $args["<BAM>"]
+    var
+      bam: Bam
+    open(bam, cstring($args["<BAM>"]), threads=1)
+    let cooked = cookTarget(target, bam)
+    for t in cooked.keys():
+      if debug:
+        echo "# Chromosome:" , t
+      for region in cooked[t]:
+        echo "[",t,"]\t", region.start, "\t", region.stop, "\t", region.label
+
   return 0
 
 type EKeyboardInterrupt = object of CatchableError

src/bamtocov.nim

@@ -16,7 +16,7 @@ import sets
 
 # FEATURES paper
 # ✅ TODO multi-bam report 
-# ✅ TODO quantized output 
+# ✅ TODO quantized output m
 # TODO max-min coverage?
 # TODO number of bases under X per target
 # ✅ TODO no output option, if one only wants the report

tests/batch.sh

@@ -0,0 +1,27 @@
+set -euxo pipefail
+BIN=bin/bamtocov
+touch $BIN && rm $BIN
+test="bin/bamtocov --version && bin/bamtocov -r input/regions.bed -o ciao input/mini.bam --debug"
+nim c  --colors:on --noNimblePath --path:/local/giovanni/bamtocov/nimbledeps/pkgs/hts-0.3.17 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/docopt-0.6.8 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/regex-0.19.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/unicodedb-0.9.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/lapper-0.1.7   -d:NimblePkgVersion=V1 -d:release  --opt:speed -d:danger --out:bin/bamtocov src/bamtocov.nim 2>&1 > /dev/null
+
+$test
+
+nim c  --path:/local/giovanni/bamtocov/nimbledeps/pkgs/hts-0.3.17 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/docopt-0.6.8 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/regex-0.19.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/unicodedb-0.9.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/lapper-0.1.7   -d:NimblePkgVersion=V2 -d:release  --opt:speed -d:danger --out:bin/bamtocov src/bamtocov.nim 2>&1 > /dev/null
+
+$test
+
+nim c  -d:NimblePkgVersion=V3 -d:release  --opt:speed -d:danger --out:bin/bamtocov src/bamtocov.nim 2>&1 > /dev/null
+
+$test
+
+nim c  -d:NimblePkgVersion=V4 -d:release  --opt:speed --out:bin/bamtocov src/bamtocov.nim 2>&1 > /dev/null
+
+$test
+
+nim c  -d:NimblePkgVersion=V5 --opt:speed --out:bin/bamtocov src/bamtocov.nim 2>&1 > /dev/null
+
+$test
+
+nim c  -d:NimblePkgVersion=V6 --out:bin/bamtocov src/bamtocov.nim 2>&1 > /dev/null
+
+$test

tests/shpec/bamtocov.sh

@@ -12,13 +12,18 @@ describe "Coverage tools tested by Shpec"
     DATADIR="$( cd -- "$( dirname -- "$SELFDIR"/../../input/mini.bam )" &> /dev/null && pwd )"
   fi
 
+  it "Binary found"
+    assert file_present "$BINDIR/bamtocov"
+    assert file_present "$BINDIR/bamtocounts"
+  end
   # PROGRAM: bamtocov
   describe "BamToCov"
     it "Binary exist"
         assert file_present "$BINDIR"/bamtocov
     end
-    it "Version emitted is 2.x"
-      VERSION=$("$BINDIR"/bamtocov --version)
+    VERSION=$("$BINDIR"/bamtocov --version)
+    it "Version emitted is 2.x [$VERSION]"
+
       assert glob "$VERSION" "2.*"
     end
 
@@ -47,13 +52,13 @@ describe "Coverage tools tested by Shpec"
         assert file_present $TMPFILE
       end    
 
-      # it "Target BED: Report file ($TMPFILE)"
-      #   LINES=$(cat "$TMPFILE" | wc -l)
-      #   STRING=$(cat "$TMPFILE")
-      #   assert equal $LINES 7
-      #   assert grep  "${STRING}" "shared1_10"
-      #   rm $TMPFILE
-      # end
+      it "Target BED: Report file ($TMPFILE)"
+        LINES=$(cat "$TMPFILE" | wc -l)
+        STRING=$(cat "$TMPFILE")
+        assert equal $LINES 7
+        assert glob  "${STRING}" "interval*"
+        rm $TMPFILE
+      end
 
     end