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Swich to the system min and max functions and remove the version from obiutils

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Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
This commit is contained in:
Eric Coissac
2024-05-30 08:27:24 +02:00
parent 98b3bc2a8c
commit dd9307a4cd
12 changed files with 58 additions and 145 deletions
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81
pkg/obiformats/fastqseq_read.go
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@ -100,87 +100,6 @@ func _EndOfLastFastqEntry(buffer []byte) int {
return cut
}
func lastFastqCut(buffer []byte) ([]byte, []byte) {
imax := len(buffer)
cut := imax
state := 0
restart := imax - 1
for i := restart; i >= 0 && state < 7; i-- {
C := buffer[i]
is_end_of_line := C == '\r' || C == '\n'
is_space := C == ' ' || C == '\t'
is_sep := is_space || is_end_of_line
switch state {
case 0:
if C == '+' {
// Potential start of quality part step 1
state = 1
restart = i
}
case 1:
if is_end_of_line {
// Potential start of quality part step 2
state = 2
} else {
// it was not the start of quality part
state = 0
i = restart
}
case 2:
if is_sep {
// Potential start of quality part step 2 (stay in the same state)
state = 2
} else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
// End of the sequence
state = 3
} else {
// it was not the start of quality part
state = 0
i = restart
}
case 3:
if is_end_of_line {
// Entrering in the header line
state = 4
} else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
// progressing along of the sequence
state = 3
} else {
// it was not the sequence part
state = 0
i = restart
}
case 4:
if is_end_of_line {
state = 4
} else {
state = 5
}
case 5:
if is_end_of_line {
// It was not the header line
state = 0
i = restart
} else if C == '@' {
state = 6
cut = i
}
case 6:
if is_end_of_line {
state = 7
} else {
state = 0
i = restart
}
}
}
if state == 7 {
return buffer[:cut], bytes.Clone(buffer[cut:])
}
return []byte{}, buffer
}
func _ParseFastqFile(source string,
input ChannelSeqFileChunk,
out obiiter.IBioSequence,