First attempt for obiconsensus... The graph traversing algorithm is too simple

Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba

pkg/obitools/obiconvert/options.go

@@ -30,6 +30,8 @@ var __compressed__ = false
 var __output_file_name__ = "-"
 var __paired_file_name__ = ""
 
+var __full_file_batch__ = false
+
 func InputOptionSet(options *getoptions.GetOpt) {
 	// options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
 	// 	options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
@@ -201,3 +203,10 @@ func CLIHasPairedFile() bool {
 func CLIPairedFileName() string {
 	return __paired_file_name__
 }
+
+func SetFullFileBatch() {
+	__full_file_batch__ = true
+}
+func FullFileBatch() bool {
+	return __full_file_batch__
+}

pkg/obitools/obiconvert/sequence_reader.go

@@ -99,9 +99,13 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
 
 	opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
+	opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
+
 
 	if len(filenames) == 0 {
 		log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
+		opts = append(opts, obiformats.OptionsSource("stdin"))
+
 		switch CLIInputFormat() {
 		case "ecopcr":
 			iterator = obiformats.ReadEcoPCR(os.Stdin, opts...)
@@ -121,7 +125,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 
 		switch CLIInputFormat() {
 		case "ecopcr":
-			reader = obiformats.ReadEcoPCRBatchFromFile
+			reader = obiformats.ReadEcoPCRFromFile
 		case "embl":
 			reader = obiformats.ReadEMBLFromFile
 		case "genbank":