optimize sequence readers and patch a bug in the format guesser

Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5

pkg/obitools/obipcr/options.go

@@ -18,6 +18,7 @@ var _MinimumLength = 0
 var _MaximumLength = -1
 var _Fragmented = false
 var _Delta = -1
+var _OnlyFull = false
 
 // PCROptionSet defines every options related to a simulated PCR.
 //
@@ -58,6 +59,9 @@ func PCROptionSet(options *getoptions.GetOpt) {
 	options.IntVar(&_Delta, "delta", -1,
 		options.Alias("D"),
 		options.Description("Lenght of the sequence fragment to be added to the barcode extremities."))
+	options.BoolVar(&_OnlyFull, "only-complete-flanking", false,
+		options.Description("Only fragments with complete flanking sequences are printed."))
+
 }
 
 // OptionSet adds to the basic option set every options declared for
@@ -131,3 +135,7 @@ func CLIWithExtension() bool {
 func CLIExtension() int {
 	return _Delta
 }
+
+func CLIOnlyFull() bool {
+	return _OnlyFull
+}

pkg/obitools/obipcr/pcr.go

@@ -24,6 +24,7 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 			CLIReversePrimer(),
 			CLIAllowedMismatch(),
 		),
+		obiapat.OptionOnlyFullExtension(CLIOnlyFull()),
 	)
 
 	if CLIMinLength() > 0 {