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Patch a bug in the fasq reader allowing to read only lower case sequence files

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Former-commit-id: f19f3812f48b215cdc5d0fdb8a39f0cd4bb5289b
This commit is contained in:
Eric Coissac
2023-11-10 09:10:54 +01:00
parent 4017e213e9
commit 677775bf04
1 changed files with 2 additions and 6 deletions
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8
pkg/obiformats/fastqseq_read.go
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@ -45,7 +45,7 @@ func lastFastqCut(buffer []byte) ([]byte, []byte) {
if is_sep { if is_sep {
// Potential start of quality part step 2 (stay in the same state) // Potential start of quality part step 2 (stay in the same state)
state = 2 state = 2
} else if (C >= 'a' && C <= 'z') || C == '-' || C == '.' { } else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
// End of the sequence // End of the sequence
state = 3 state = 3
} else { } else {
@ -57,7 +57,7 @@ func lastFastqCut(buffer []byte) ([]byte, []byte) {
if is_end_of_line { if is_end_of_line {
// Entrering in the header line // Entrering in the header line
state = 4 state = 4
} else if (C >= 'a' && C <= 'z') || C == '-' || C == '.' { } else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
// progressing along of the sequence // progressing along of the sequence
state = 3 state = 3
} else { } else {
@ -115,10 +115,6 @@ func FastqChunkReader(r io.Reader, size int) (chan FastxChunk, error) {
end := []byte{} end := []byte{}
for err == nil && n > 0 { for err == nil && n > 0 {
// fmt.Println("============end=========================")
// fmt.Println(string(end))
// fmt.Println("------------buff------------------------")
// fmt.Println(string(buff))
buff = Concatenate(end, buff) buff = Concatenate(end, buff)
// fmt.Println("------------buff--pasted----------------") // fmt.Println("------------buff--pasted----------------")
// fmt.Println(string(buff)) // fmt.Println(string(buff))