Fixing help parsing to make it so error messages don't appear if you …

…provide the help flag as the first input; fixing nimble file to compile poaV2 before build step

conduit.nimble

@@ -1,6 +1,6 @@
 # Package
 
-version       = "0.1.0"
+version       = "0.1.2"
 author        = "Nathan Roach"
 description   = "De novo transcriptome assembler"
 license       = "GPLv2"
@@ -16,4 +16,9 @@ before install:
   withDir "src/poaV2":
     exec "make"
 
+before build:
+  echo "Building poaV2"
+  withDir "src/poaV2":
+    exec "make"
+
 bin = @["conduit", "conduitUtils", "conduit_clustering"]

src/conduit.nim

@@ -86,7 +86,7 @@ type
 
 
 proc conduitVersion() : string =
-  return "CONDUIT Version 0.1.1 by Nathan Roach ( nroach2@jhu.edu, https://github.com/NatPRoach/conduit/ )"
+  return "CONDUIT Version 0.1.2 by Nathan Roach ( nroach2@jhu.edu, https://github.com/NatPRoach/conduit/ )"
 
 proc writeDefaultHelp() = 
   echo "CONDUIT - CONsensus Decomposition Utility In Transcriptome-assembly:"
@@ -629,9 +629,16 @@ proc parseOptions() : ConduitOptions =
   for kind, key, val in getopt():
     # echo kind," ", key," ", val
     if i == 0:
-      mode = key
-      i += 1
-      continue
+      if kind == cmdArgument:
+        mode = key
+        i += 1
+        continue
+      else:
+        if key == "h" or key == "help":
+          mode = "help"
+        helpFlag = true
+        runFlag = false
+        break
     if i == 1:
       helpFlag = false
     i += 1
@@ -1022,7 +1029,7 @@ proc parseOptions() : ConduitOptions =
       else:
         helpFlag = true
         break
-  if clustersDirectory == "":
+  if clustersDirectory == "" and mode != "help" and not helpFlag:
     echo "ERROR - <clusters directory> must be specified"
     helpFlag = true
     runFlag = false
@@ -1033,6 +1040,9 @@ proc parseOptions() : ConduitOptions =
         writeNanoHelp()
       of "hybrid":
         writeHybridHelp()
+      of "help":
+        writeDefaultHelp()
+        quit(QuitSuccess)
       else:
         echo "ERROR - first argument must specify correction mode, \"nano\" or \"hybrid\""
         writeDefaultHelp()

src/conduitUtils.nim

@@ -59,7 +59,7 @@ type
 
 
 proc conduitUtilsVersion() : string =
-  return "CONDUIT Utilities Version 0.1.1 by Nathan Roach ( nroach2@jhu.edu, https://github.com/NatPRoach/conduit/ )"
+  return "CONDUIT Utilities Version 0.1.2 by Nathan Roach ( nroach2@jhu.edu, https://github.com/NatPRoach/conduit/ )"
 
 
 proc writeDefaultHelp() = 
@@ -1232,9 +1232,17 @@ proc parseOptions() : UtilOptions =
   for kind, key, val in getopt():
     # echo kind," ", key," ", val
     if i == 0:
-      mode = key
-      i += 1
-      continue
+      if kind == cmdArgument:
+        mode = key
+        i += 1
+        continue
+      else:
+        if key == "h" or key == "help":
+          mode = "help"
+        helpFlag = true
+        runFlag = false
+        break
+
     if i == 1:
       helpFlag = false
     i += 1
@@ -1392,6 +1400,9 @@ proc parseOptions() : UtilOptions =
         writeCallNovelNonCanonicalHelp()
       of "callOverlapping":
         writeCallOverlappingHelp()
+      of "help":
+        writeDefaultHelp()
+        quit(QuitSuccess)
       else:
         echo "ERROR - first argument must specify utility function"
         writeDefaultHelp()

src/conduit_clustering.nim

@@ -38,7 +38,7 @@ type
 # TODO -   Possibly change uint32 to uint64 where necessary.
 # TODO - Reevaluate before publication.
 proc conduitClusterVersion() : string =
-  return "CONDUIT Clustering Version 0.1.1 by Nathan Roach ( nroach2@jhu.edu," &
+  return "CONDUIT Clustering Version 0.1.2 by Nathan Roach ( nroach2@jhu.edu," &
     " https://github.com/NatPRoach/conduit/ )"
 
 
@@ -339,7 +339,7 @@ proc parseClusteringOptions() : ClusteringOptions =
             break
         last = ""
 
-  if file == "":
+  if file == "" and not helpFlag:
     echo "ERROR - clustering requires an input BAM file"
     helpFlag = true
     runFlag = false