new --version option and qualities method in obiscript

Former-commit-id: 7b0ce2901785d5c7494dec3a7a95d1fc5dc4a52b

Release-notes.md

@@ -2,13 +2,20 @@
 
 ## Latest changes
 
+### New features
+
+-   A new option **--version** has been added to every obitools command.
+    It will print the version of the command.
+-   In `obiscript` a `qualities` method has been added to retrieve or set the quality scores from a
+    BioSequence object.         
+
 ### Bug
 
 -   In `obitag`, correct the wrong assignation of the **obitag_bestmatch** attribute.
 
 ## April 2nd, 2024. Release 4.2.0
 
-### New feature
+### New features
 -   A new OBITools named `obiscript` allows to process each sequence according to a Lua script. This is 
     an experimental tool. The **--template** option allows for generating an example script on the `stdout`.
 

pkg/obilua/lua_push_interface.go

@@ -37,15 +37,17 @@ func pushInterfaceToLua(L *lua.LState, val interface{}) {
 	case []string:
 		pushSliceStringToLua(L, v)
 	case []int:
-		pushSliceIntToLua(L, v)
+		pushSliceNumericToLua(L, v)
+	case []byte:
+		pushSliceNumericToLua(L, v)
 	case []float64:
-		pushSliceFloat64ToLua(L, v)
+		pushSliceNumericToLua(L, v)
 	case []bool:
 		pushSliceBoolToLua(L, v)
 	case nil:
 		L.Push(lua.LNil)
 	default:
-		log.Fatalf("Cannot deal with value %v", val)
+		log.Fatalf("Cannot deal with value (%T) : %v", val, val)
 	}
 }
 
@@ -163,6 +165,21 @@ func pushSliceIntToLua(L *lua.LState, slice []int) {
 	L.Push(luaTable)
 }
 
+func pushSliceNumericToLua[T float64 | int | byte](L *lua.LState, slice []T) {
+	// Create a new Lua table
+	luaTable := L.NewTable()
+
+	// Iterate over the Go slice and set the elements in the Lua table
+	for _, value := range slice {
+		// Append the value to the Lua table
+		// Lua is 1-indexed, so we use the length of the table + 1 as the next index
+		luaTable.Append(lua.LNumber(value))
+	}
+
+	// Push the Lua table onto the stack
+	L.Push(luaTable)
+}
+
 // pushSliceStringToLua creates a new Lua table and sets the elements in the table from the given Go slice. It then pushes the Lua table onto the stack.
 //
 // L *lua.LState - The Lua state

pkg/obilua/lua_table.go

@@ -1,6 +1,10 @@
 package obilua
 
-import lua "github.com/yuin/gopher-lua"
+import (
+	"log"
+
+	lua "github.com/yuin/gopher-lua"
+)
 
 func Table2Interface(interpreter *lua.LState, table *lua.LTable) interface{} {
 	// <EC> 07/03/2024: il y a sans doute plus efficace mais pour l'instant
@@ -48,6 +52,39 @@ func Table2Interface(interpreter *lua.LState, table *lua.LTable) interface{} {
 	}
 }
 
+func Table2ByteSlice(interpreter *lua.LState, table *lua.LTable) []byte {
+	isArray := true
+	table.ForEach(func(key, value lua.LValue) {
+		if _, ok := key.(lua.LNumber); !ok {
+			isArray = false
+		}
+	})
+
+	if isArray {
+		val := make([]byte, table.Len())
+
+		for i := 1; i <= table.Len(); i++ {
+			v := table.RawGetInt(i)
+			switch v.Type() {
+			case lua.LTNumber:
+				if x:=float64(v.(lua.LNumber)); x <=255 {
+					val[i-1] = byte(x)
+				} else {
+					log.Fatalf("LUA: Value %f at index %d is to large to be converted to byte", x,i)
+				}
+			default:
+				log.Fatalf("LUA: Value %v at index %d cannot be converted to byte", v,i)
+			}
+		}
+
+		return val
+	}
+
+	log.Fatalf("LUA: Value %v cannot be converted to []byte", table)
+
+	return nil
+}
+
 // 	}
 
 // 	return nil

pkg/obilua/obiseq.go

@@ -48,6 +48,7 @@ func newObiSeq(luaState *lua.LState) int {
 var bioSequenceMethods = map[string]lua.LGFunction{
 	"id":            bioSequenceGetSetId,
 	"sequence":      bioSequenceGetSetSequence,
+	"qualities":     bioSequenceGetSetQualities,
 	"definition":    bioSequenceGetSetDefinition,
 	"count":         bioSequenceGetSetCount,
 	"taxid":         bioSequenceGetSetTaxid,
@@ -99,6 +100,29 @@ func bioSequenceGetSetSequence(luaState *lua.LState) int {
 	return 1
 }
 
+func bioSequenceGetSetQualities(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	if luaState.GetTop() == 2 {
+		ud := luaState.CheckAny(2)
+
+		//
+		// Perhaps the code needs some type checking on ud.Value
+		// It's a first test
+		//
+
+		if v, ok := ud.(*lua.LTable); ok {
+			s.SetQualities(Table2ByteSlice(luaState, v))
+			return 0
+		}
+
+	}
+
+	value := []byte(s.Qualities())
+	pushInterfaceToLua(luaState, value)
+
+	return 1
+}
+
 func bioSequenceGetSetDefinition(luaState *lua.LState) int {
 	s := checkBioSequence(luaState)
 	if luaState.GetTop() == 2 {

pkg/obioptions/options.go

@@ -21,6 +21,7 @@ var _BatchSize = 5000
 var _Pprof = false
 var _Quality_Shift_Input = 33
 var _Quality_Shift_Output = 33
+var _Version = "4.2.1"
 
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
 
@@ -30,6 +31,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 	options.SetMode(getoptions.Bundling)
 	options.SetUnknownMode(getoptions.Fail)
 	options.Bool("help", false, options.Alias("h", "?"))
+	options.Bool("version", false)
 	options.BoolVar(&_Debug, "debug", false)
 	options.BoolVar(&_Pprof, "pprof", false)
 
@@ -62,6 +64,11 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 			os.Exit(1)
 		}
 
+		if options.Called("version") {
+			fmt.Fprintf(os.Stderr, "obitools version %s\n", _Version)
+			os.Exit(0)
+		}
+
 		log.SetLevel(log.InfoLevel)
 		if options.Called("debug") {
 			log.SetLevel(log.DebugLevel)