Add the -D (--delta) option to obipcr

Former-commit-id: 753079807faaddb23e03fd6350125bfa67f98c7f

Release-notes.md

@@ -2,6 +2,17 @@
 
 ## Latest changes
 
+### Enhancement
+
+- A new completely rewritten GO version of the fastq and fasta parser is now used instead of the original C version. 
+- A new file format guesser is now implemented. This is a first step towards allowing new formats to be managed by obitools.
+- New way of handling header definitions of fasta and fastq formats with JSON headers.
+  The sequence definition is now printed in new files as an attribute of the json header named "definition".
+- The -D (--delta) option has been added to `obipcr`. It allows to extract flanking sequences of the barcode.
+    + If -D is not set, the output sequence is the barcode itself without the priming sites. 
+    + If -D is set to 0, the output sequence is the barcode with the priming sites.
+    + When -D is set to ### (where ### is an integer), the output sequence is the barcode with the priming sites.  
+      and ### base pairs of flanking sequences.
 ### Becareful
 
 GO 1.21.0 is out, and it includes new functionalities which are used in the OBITools4 code.

pkg/obiapat/pcr.go

@@ -13,6 +13,7 @@ type _Options struct {
 	circular        bool
 	forwardError    int
 	reverseError    int
+	extension       int
 	batchSize       int
 	parallelWorkers int
 	forward         ApatPattern
@@ -31,6 +32,15 @@ type Options struct {
 // declaring options.
 type WithOption func(Options)
 
+func (options Options) HasExtension() bool {
+	return options.pointer.extension > -1
+
+}
+
+func (options Options) Extension() int {
+	return options.pointer.extension
+}
+
 // MinLength method returns minimum length of
 // the searched amplicon (length of the primers
 // excluded)
@@ -85,6 +95,7 @@ func MakeOptions(setters []WithOption) Options {
 		maxLength:       0,
 		forwardError:    0,
 		reverseError:    0,
+		extension:       -1,
 		circular:        false,
 		parallelWorkers: 4,
 		batchSize:       100,
@@ -148,6 +159,19 @@ func OptionForwardPrimer(primer string, max int) WithOption {
 	return f
 }
 
+// OptionWithExtension sets the length of the extension to be added to the sequence.
+//
+// An negative value indicates that no extension is added
+// The extension parameter is an integer that represents the extension value to be set.
+// The returned function is of type WithOption.
+func OptionWithExtension(extension int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.extension = extension
+	})
+
+	return f
+}
+
 // OptionForwardError sets the number of
 // error allowed when matching the forward
 // primer.
@@ -253,8 +277,16 @@ func _Pcr(seq ApatSequence,
 							if length > 0 && // For when primers touch or overlap
 								(opt.MinLength() == 0 || length >= opt.MinLength()) &&
 								(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
-								amplicon, _ := seq.pointer.reference.Subsequence(fm[1], rm[0], opt.pointer.circular)
-								log.Debugf("seq length : %d capacity : %d",amplicon.Len(),cap(amplicon.Sequence()))
+								var from, to int
+								if opt.HasExtension() {
+									from = fm[0] - opt.Extension()
+									to = rm[1] + opt.Extension()
+								} else {
+									from = fm[1]
+									to = rm[0]
+								}
+								amplicon, _ := seq.pointer.reference.Subsequence(from, to, opt.pointer.circular)
+								log.Debugf("seq length : %d capacity : %d", amplicon.Len(), cap(amplicon.Sequence()))
 								annot := amplicon.Annotations()
 								obiutils.MustFillMap(annot, seq.pointer.reference.Annotations())
 
@@ -287,7 +319,7 @@ func _Pcr(seq ApatSequence,
 	}
 
 	forwardMatches = reverse.FindAllIndex(seq, 0, -1)
-	
+
 	if forwardMatches != nil {
 
 		begin := forwardMatches[0][0]
@@ -303,7 +335,6 @@ func _Pcr(seq ApatSequence,
 		}
 
 		reverseMatches := cfwd.FindAllIndex(seq, begin, length)
-		
 
 		if reverseMatches != nil {
 			for _, fm := range forwardMatches {
@@ -331,7 +362,15 @@ func _Pcr(seq ApatSequence,
 							if length > 0 && // For when primers touch or overlap
 								(opt.MinLength() == 0 || length >= opt.MinLength()) &&
 								(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
-								amplicon, _ := seq.pointer.reference.Subsequence(fm[1], rm[0], opt.pointer.circular)
+								var from, to int
+								if opt.HasExtension() {
+									from = fm[0] - opt.Extension()
+									to = rm[1] + opt.Extension()
+								} else {
+									from = fm[1]
+									to = rm[0]
+								}
+								amplicon, _ := seq.pointer.reference.Subsequence(from, to, opt.pointer.circular)
 								amplicon = amplicon.ReverseComplement(true)
 
 								annot := amplicon.Annotations()
@@ -401,13 +440,13 @@ func _PCRSlice(sequences obiseq.BioSequenceSlice,
 		for _, sequence := range sequences[1:] {
 			seq, _ = MakeApatSequence(sequence, options.Circular(), seq)
 			amplicons = _Pcr(seq, options)
-			
+
 			if len(amplicons) > 0 {
 				results = append(results, amplicons...)
 			}
 		}
 
-	    //log.Debugln(AllocatedApaSequences())
+		//log.Debugln(AllocatedApaSequences())
 
 		// seq.Free()
 	}
@@ -433,7 +472,7 @@ func PCRSliceWorker(options ...WithOption) obiseq.SeqSliceWorker {
 
 	opt := MakeOptions(options)
 	worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
-		result :=  _PCRSlice(sequences, opt)
+		result := _PCRSlice(sequences, opt)
 		sequences.Recycle(true)
 		return result
 	}

pkg/obitools/obipcr/options.go

@@ -17,6 +17,7 @@ var _AllowedMismatch = 0
 var _MinimumLength = 0
 var _MaximumLength = -1
 var _Fragmented = false
+var _Delta = -1
 
 // PCROptionSet defines every options related to a simulated PCR.
 //
@@ -54,6 +55,9 @@ func PCROptionSet(options *getoptions.GetOpt) {
 		options.Alias("L"),
 		options.Required("You must indicate the maximum size of the amplicon (excluded primer length)"),
 		options.Description("Maximum length of the barcode (primers excluded)."))
+	options.IntVar(&_Delta, "delta", -1,
+		options.Alias("D"),
+		options.Description("Lenght of the sequence fragment to be added to the barcode extremities."))
 }
 
 // OptionSet adds to the basic option set every options declared for
@@ -119,3 +123,11 @@ func CLIMaxLength() int {
 func CLIFragmented() bool {
 	return _Fragmented
 }
+
+func CLIWithExtension() bool {
+	return _Delta >= 0
+}
+
+func CLIExtension() int {
+	return _Delta
+}

pkg/obitools/obipcr/pcr.go

@@ -30,6 +30,10 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 		opts = append(opts, obiapat.OptionMinLength(CLIMinLength()))
 	}
 
+	if CLIWithExtension() {
+		opts = append(opts, obiapat.OptionWithExtension(CLIExtension()))
+	}
+
 	opts = append(opts, obiapat.OptionMaxLength(CLIMaxLength()))
 
 	if CLICircular() {