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Start of implementing binary file format

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This commit is contained in:
Eric Coissac
2022-02-07 11:57:08 +01:00
parent d5a1a191f8
commit 27556ce81f
2 changed files with 105 additions and 2 deletions
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2
pkg/obiseq/predicate.go
View File

@ -2,7 +2,6 @@ package obiseq
type SequencePredicate func(BioSequence) bool type SequencePredicate func(BioSequence) bool
func (predicate1 SequencePredicate) And(predicate2 SequencePredicate) SequencePredicate { func (predicate1 SequencePredicate) And(predicate2 SequencePredicate) SequencePredicate {
f := func(sequence BioSequence) bool { f := func(sequence BioSequence) bool {
return predicate1(sequence) && predicate2(sequence) return predicate1(sequence) && predicate2(sequence)
@ -74,4 +73,3 @@ func IsShorterOrEqualTo(length int) SequencePredicate {
return f return f
} }

105
pkg/obiseq/surge.go Normal file
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@ -0,0 +1,105 @@
package obiseq
import "github.com/renproject/surge"
func (sequence BioSequence) SizeHint() int {
return surge.SizeHintString(sequence.sequence.id) +
surge.SizeHintString(sequence.sequence.definition) +
surge.SizeHintBytes(sequence.sequence.sequence) +
surge.SizeHintBytes(sequence.sequence.qualities) +
surge.SizeHintBytes(sequence.sequence.feature) +
surge.SizeHint(sequence.sequence.annotations)
}
func (sequence BioSequence) Marshal(buf []byte, rem int) ([]byte, int, error) {
var err error
if buf, rem, err = surge.MarshalString(sequence.sequence.id, buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.MarshalString(sequence.sequence.definition, buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.MarshalBytes(sequence.sequence.sequence, buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.MarshalBytes(sequence.sequence.qualities, buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.MarshalBytes(sequence.sequence.feature, buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.Marshal(sequence.sequence.annotations, buf, rem); err != nil {
return buf, rem, err
}
return buf, rem, err
}
// Unmarshal is the opposite of Marshal, and requires
// a pointer receiver.
func (sequence *BioSequence) Unmarshal(buf []byte, rem int) ([]byte, int, error) {
var err error
if buf, rem, err = surge.UnmarshalString(&(sequence.sequence.id), buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.UnmarshalString(&(sequence.sequence.definition), buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.UnmarshalBytes(&(sequence.sequence.sequence), buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.UnmarshalBytes(&(sequence.sequence.qualities), buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.UnmarshalBytes(&(sequence.sequence.feature), buf, rem); err != nil {
return buf, rem, err
}
if buf, rem, err = surge.Unmarshal(&(sequence.sequence.annotations), buf, rem); err != nil {
return buf, rem, err
}
return buf, rem, err
}
func (sequences BioSequenceSlice) SizeHint() int {
size := surge.SizeHintI64
for _, s := range sequences {
size += s.SizeHint()
}
return size
}
func (sequences BioSequenceSlice) Marshal(buf []byte, rem int) ([]byte, int, error) {
var err error
if buf, rem, err = surge.MarshalI64(int64(len(sequences)), buf, rem); err != nil {
return buf, rem, err
}
for _, s := range sequences {
if buf, rem, err = s.Marshal(buf, rem); err != nil {
return buf, rem, err
}
}
return buf, rem, err
}
func (sequences *BioSequenceSlice) Unmarshal(buf []byte, rem int) ([]byte, int, error) {
var err error
var length int64
if buf, rem, err = surge.UnmarshalI64(&length, buf, rem); err != nil {
return buf, rem, err
}
*sequences = make(BioSequenceSlice, length)
for i := 0; i < int(length); i++ {
if buf, rem, err = ((*sequences)[i]).Unmarshal(buf, rem); err != nil {
return buf, rem, err
}
}
return buf, rem, err
}