From c11189bab9a9e8e9fe9258cec8d1a8b8e2f97f18 Mon Sep 17 00:00:00 2001
From: nanguage <nanguage@yahoo.com>
Date: Sun, 28 Jan 2018 22:05:21 +0800
Subject: [PATCH] use parseopt2 replace docopt

---
 src/argparse.nim | 134 +++++++++++++++++++++++++++++++++++++++++++++++
 src/main.nim     |   5 +-
 2 files changed, 137 insertions(+), 2 deletions(-)
 create mode 100644 src/argparse.nim

diff --git a/src/argparse.nim b/src/argparse.nim
new file mode 100644
index 0000000..6360127
--- /dev/null
+++ b/src/argparse.nim
@@ -0,0 +1,134 @@
+import tables
+import parseopt2
+
+type
+
+  ValueKind* = enum
+    vkNone,
+    vkBool,
+    vkStr,
+
+  Value* = object
+    case kind*: ValueKind
+    of vkNone:
+      nil
+    of vkBool:
+      bool_v: bool
+    of vkStr:
+      str_v: string
+
+
+converter to_bool*(v: Value): bool =
+  case v.kind
+  of vkNone:
+    false
+  of vkBool:
+    v.bool_v
+  of vkStr:
+    v.str_v != nil and v.str_v.len > 0 
+
+
+proc val(): Value = Value(kind: vkNone)
+proc val(v: bool): Value = Value(kind: vkBool, bool_v: v)
+proc val(v: string): Value = Value(kind: vkStr, str_v: v)
+
+
+proc `$`*(v: Value): string =
+  case v.kind
+  of vkNone:
+    "nil"
+  of vkBool:
+    $v.bool_v
+  of vkStr:
+    v.str_v
+
+
+proc parse_args*(doc: string): Table[string, Value] =
+
+  result = {
+    "fq": val(),
+    "fa": val(),
+    "sam": val(),
+    "<file>": val(),
+    "color-atla": val(),
+    "example-config": val(),
+
+    "--phred": val(),
+    "--hist": val(),
+    "--delimiter": val(),
+    "--multiline": val(),
+    "--color": val(),
+    "--type": val(),
+    "--config-file": val(),
+  }.toTable()
+
+  var arg_ct: int = 0
+
+  for kind, key, value in getopt():
+    when not defined(release):
+      stderr.write(($kind) & " " & ($key) & " " & ($value) & "\n")
+      stderr.flushFile()
+    case kind
+    of cmdArgument:
+      case arg_ct:
+      of 0:
+        case key:
+        of "fq":
+          result["fq"] = val(true)
+        of "fa":
+          result["fa"] = val(true)
+        of "sam":
+          result["sam"] = val(true)
+        of "color-atla":
+          result["color-atla"] = val(true)
+          return result
+        of "example-config":
+          result["example-config"] = val(true)
+          return result
+      of 1:
+        result["<file>"] = val(key)
+      else:
+        echo doc
+        quit(1)
+      inc arg_ct
+    of cmdShortOption:
+      case key
+      of "h":
+        echo doc
+        quit(0)
+      if key == "" and value == "":
+        result["<file>"] = val("-")
+        inc arg_ct
+    of cmdLongOption:
+      case key:
+      of "h", "help":
+        echo doc
+        quit(0)
+      of "phred":
+        result["--phred"] = val(value)
+      of "hist":
+        result["--hist"] = val(value)
+      of "delimiter":
+        result["--delimiter"] = val(value)
+      of "multiline":
+        if value != "":
+          result["--multiline"] = val(value)
+        else:
+          result["--multiline"] = val("yes")
+      of "color":
+        result["--color"] = val(value)
+      of "type":
+        result["--type"] = val(value)
+      of "config-file":
+        result["--config-file"] = val(value)
+    of cmdEnd:
+      discard
+    
+  if (not result["fq"]) and (not result["fa"]) and (not result["sam"]) and
+     (not result["example-config"]) and (not result["color-atla"]):
+    echo doc
+    quit(1)
+
+
+when isMainModule:
+  discard
\ No newline at end of file
diff --git a/src/main.nim b/src/main.nim
index 877faf1..adf8c3d 100644
--- a/src/main.nim
+++ b/src/main.nim
@@ -21,8 +21,9 @@ Options:
 """
 
 import os
+import tables
 
-import docopt
+import argparse
 
 import color_atla
 import fastq_utils
@@ -30,7 +31,7 @@ import fasta_utils
 import sam_utils
 import configs
 
-let args = docopt(doc, version = "BioView 0.0.0")
+var args = parse_args(doc)
 
 if args["color-atla"]:
   print_color_atla()