Correct a bug in the fastq reader affecting the quality of the last record of each chunk

Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
This commit is contained in:
Eric Coissac
2024-06-04 11:57:16 +02:00
parent 411124d1b3
commit aa42df326a
6 changed files with 104 additions and 42 deletions

View File

@@ -15,6 +15,17 @@ var _BioSequenceByteSlicePool = sync.Pool{
},
}
// RecycleSlice recycles a byte slice by clearing its contents and returning it
// to a pool if it is small enough.
//
// Parameters: - s: a pointer to a byte slice that will be recycled.
//
// This function first checks if the input slice is not nil and has a non-zero
// capacity. If so, it clears the contents of the slice by setting its length to
// 0. Then, it checks if the capacity of the slice is less than or equal to
// 1024. If it is, the function puts the slice into a pool for reuse. If the
// capacity is 0 or greater than 1024, the function does nothing. If the input
// slice is nil or has a zero capacity, the function logs a panic message.
func RecycleSlice(s *[]byte) {
if s != nil && cap(*s) > 0 {
*s = (*s)[:0]
@@ -27,9 +38,22 @@ func RecycleSlice(s *[]byte) {
}
}
// It returns a slice of bytes from a pool of slices.
// GetSlice returns a byte slice with the specified capacity.
//
// the slice can be prefilled with the provided values
// The function first checks if the capacity is less than or equal to 1024. If it is,
// it retrieves a byte slice from the _BioSequenceByteSlicePool. If the retrieved
// slice is nil, has a nil underlying array, or has a capacity less than the
// specified capacity, a new byte slice is created with the specified capacity.
// If the capacity is greater than 1024, a new byte slice is created with the
// specified capacity.
//
// The function returns the byte slice.
//
// Parameters:
// - capacity: the desired capacity of the byte slice.
//
// Return type:
// - []byte: the byte slice with the specified capacity.
func GetSlice(capacity int) []byte {
p := (*[]byte)(nil)
if capacity <= 1024 {