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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
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@@ -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
}