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Adds the reading of the options through the csv formated ngsfilter configuration file

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Former-commit-id: 0e9a13689da2ba45293c7de1f728d3d0d34d3238
This commit is contained in:
Eric Coissac
2024-06-04 22:57:07 +02:00
parent c8ad96f5e6
commit 87a7219ab4
3 changed files with 171 additions and 19 deletions
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132
pkg/obiformats/ngsfilter_read.go
View File

@ -226,7 +226,7 @@ func ReadOldNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
}
var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, values ...string){
"@spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
"spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @spacer parameter")
@ -251,6 +251,108 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
log.Fatalln("Invalid value for @spacer parameter")
}
},
"forward_spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @forward_spacer parameter")
case 1:
spacer, err := strconv.Atoi(values[0])
if err != nil {
log.Fatalln("Invalid value for @forward_spacer parameter")
}
library.SetForwardTagSpacer(spacer)
default:
log.Fatalln("Invalid value for @forward_spacer parameter")
}
},
"reverse_spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @reverse_spacer parameter")
case 1:
spacer, err := strconv.Atoi(values[0])
if err != nil {
log.Fatalln("Invalid value for @reverse_spacer parameter")
}
library.SetReverseTagSpacer(spacer)
default:
log.Fatalln("Invalid value for @reverse_spacer parameter")
}
},
"tag_delimiter": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @tag_delimiter parameter")
case 1:
library.SetTagDelimiter([]byte(values[0])[0])
case 2:
library.SetTagDelimiterFor(values[0], []byte(values[1])[0])
default:
log.Fatalln("Invalid value for @tag_delimiter parameter")
}
},
"forward_tag_delimiter": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @forward_tag_delimiter parameter")
case 1:
library.SetForwardTagDelimiter([]byte(values[0])[0])
default:
log.Fatalln("Invalid value for @forward_tag_delimiter parameter")
}
},
"reverse_tag_delimiter": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @reverse_tag_delimiter parameter")
case 1:
library.SetReverseTagDelimiter([]byte(values[0])[0])
default:
log.Fatalln("Invalid value for @reverse_tag_delimiter parameter")
}
},
"matching": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @matching parameter")
case 1:
if err := library.SetMatching(values[0]); err != nil {
log.Fatalf("Invalid value %s for @matching parameter", values[0])
}
default:
log.Fatalln("Invalid value for @matching parameter")
}
},
"primer_mismatches": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @primer_error parameter")
case 1:
dist, err := strconv.Atoi(values[0])
if err != nil {
log.Fatalf("Invalid value %s for @primer_error parameter", values[0])
}
library.SetAllowedMismatch(dist)
default:
log.Fatalln("Invalid value for @primer_error parameter")
}
},
"indels": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @indels parameter")
case 1:
library.SetAllowsIndels(values[0] == "true")
default:
log.Fatalln("Invalid value for @indels parameter")
}
},
}
func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
@ -272,20 +374,9 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
i := 0
for i = 0; i < len(records) && records[i][0] == "@param"; i++ {
param := records[i][1]
if len(records[i]) < 3 {
log.Fatalf("At line %d: Missing value for parameter %s", i, param)
}
data := records[i][2:]
setparam, ok := library_parameter[param]
if ok {
setparam(&ngsfilter, data...)
} else {
log.Warnf("At line %d: Skipping unknown parameter %s: %v", i, param, data)
}
}
params := records[0:i]
records = records[i:]
header := records[0]
@ -371,5 +462,20 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
}
for i := 0; i < len(params); i++ {
param := params[i][1]
if len(params[i]) < 3 {
log.Fatalf("At line %d: Missing value for parameter %s", i, param)
}
data := params[i][2:]
setparam, ok := library_parameter[param]
if ok {
setparam(&ngsfilter, data...)
} else {
log.Warnf("At line %d: Skipping unknown parameter %s: %v", i, param, data)
}
}
return &ngsfilter, nil
}

56
pkg/obingslibrary/ngslibrary.go
View File

@ -24,15 +24,20 @@ type PCR struct {
}
type NGSLibrary struct {
Matching string
Primers map[string]PrimerPair
Markers map[PrimerPair]*Marker
Matching string
Allowed_mismatches int
Allows_indels bool
Primers map[string]PrimerPair
Markers map[PrimerPair]*Marker
}
func MakeNGSLibrary() NGSLibrary {
return NGSLibrary{
Primers: make(map[string]PrimerPair, 10),
Markers: make(map[PrimerPair]*Marker, 10),
Matching: "strict",
Allowed_mismatches: 2,
Allows_indels: false,
Primers: make(map[string]PrimerPair, 10),
Markers: make(map[PrimerPair]*Marker, 10),
}
}
@ -109,6 +114,22 @@ func (library *NGSLibrary) SetTagDelimiter(delim byte) {
library.SetReverseTagDelimiter(delim)
}
func (library *NGSLibrary) SetTagDelimiterFor(primer string, delim byte) {
primers, ok := library.Primers[primer]
if ok {
marker, ok := library.Markers[primers]
if ok {
if primer == primers.Forward {
marker.SetForwardTagDelimiter(delim)
} else {
marker.SetReverseTagDelimiter(delim)
}
}
}
}
func (library *NGSLibrary) CheckTagLength() {
for _, marker := range library.Markers {
@ -132,3 +153,28 @@ func (library *NGSLibrary) CheckPrimerUnicity() error {
}
return nil
}
// SetMatching sets the matching strategy for the library.
// Returns an error if the matching strategy is invalid.
func (library *NGSLibrary) SetMatching(matching string) error {
switch matching {
case "strict", "hamming", "indel": // Valid matching strategies
library.Matching = matching
default:
return fmt.Errorf("invalid matching : %s", matching)
}
return nil
}
func (library *NGSLibrary) SetAllowedMismatch(allowed_mismatches int) {
if allowed_mismatches < 0 {
allowed_mismatches = 0
}
library.Allowed_mismatches = allowed_mismatches
}
// SetAllowsIndels sets whether the library allows indels.
// The value of the argument allows_indels is directly assigned to the library's Allows_indels field.
func (library *NGSLibrary) SetAllowsIndels(allows_indels bool) {
library.Allows_indels = allows_indels
}

2
pkg/obioptions/version.go
View File

@ -7,7 +7,7 @@ import (
// TODO: The version number is extracted from git. This induces that the version
// corresponds to the last commit, and not the one when the file will be
// commited
var _Commit = "d00f335"
var _Commit = "5affee2"
var _Version = "Release 4.2.0"
// Version returns the version of the obitools package.