obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-08 16:50:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

In obimultiplex, patch a bug when no tag are associated to a primer.

Browse Source
This commit is contained in:
Eric Coissac
2024-10-22 14:12:20 +02:00
parent 9e8a7fd9be
commit 3e00d39d47
3 changed files with 36 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
pkg/obiformats/ngsfilter_read.go
View File

@@ -536,6 +536,24 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
},
}
// ReadCSVNGSFilter reads an NGS filter configuration from a CSV file and returns
// an NGSLibrary. The CSV file must include columns for 'experiment', 'sample',
// 'sample_tag', 'forward_primer', and 'reverse_primer'. Additional columns are
// used to annotate PCR samples.
//
// Parameters:
// - reader: an io.Reader providing the CSV input.
//
// Returns:
// - A pointer to an NGSLibrary populated with the data from the CSV file.
// - An error if the CSV is malformed or required columns are missing.
//
// The function processes both data records and parameter lines starting with
// '@param'. Parameter lines configure various aspects of the library.
//
// Each row in the CSV is validated to ensure it has the correct number of columns.
// Duplicate tag pairs for the same marker result in an error. Primer unicity is
// checked, and any unknown parameters are logged as warnings.
func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
ngsfilter := obingslibrary.MakeNGSLibrary()
file := csv.NewReader(reader)
@@ -576,6 +594,7 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
extraColumns := make([]int, 0)
for i, colName := range header {
switch colName {
case "experiment":
experimentColIndex = i