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Change obiclean algorithm for a better evaluation of ratio

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This commit is contained in:
Eric Coissac
2022-08-31 20:38:03 +02:00
parent 90ba980de6
commit 6b8f4490cf
8 changed files with 371 additions and 75 deletions
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32
pkg/obiseq/biosequence.go
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@@ -199,7 +199,7 @@ func (s *BioSequence) Annotations() Annotation {
}
// A method that returns the value of the key in the annotation map.
func (s *BioSequence) Get(key string) (interface{}, bool) {
func (s *BioSequence) GetAttribute(key string) (interface{}, bool) {
var val interface{}
ok := s.annotations != nil
@@ -210,12 +210,17 @@ func (s *BioSequence) Get(key string) (interface{}, bool) {
return val, ok
}
func (s *BioSequence) SetAttribute(key string, value interface{}) {
annot := s.Annotations()
annot[key] = value
}
// A method that returns the value of the key in the annotation map.
func (s *BioSequence) GetInt(key string) (int, bool) {
func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
var val int
var err error
v, ok := s.Get(key)
v, ok := s.GetAttribute(key)
if ok {
val, err = goutils.InterfaceToInt(v)
@@ -226,9 +231,9 @@ func (s *BioSequence) GetInt(key string) (int, bool) {
}
// A method that returns the value of the key in the annotation map.
func (s *BioSequence) GetString(key string) (string, bool) {
func (s *BioSequence) GetStringAttribute(key string) (string, bool) {
var val string
v, ok := s.Get(key)
v, ok := s.GetAttribute(key)
if ok {
val = fmt.Sprint(v)
@@ -242,7 +247,7 @@ func (s *BioSequence) GetBool(key string) (bool, bool) {
var val bool
var err error
v, ok := s.Get(key)
v, ok := s.GetAttribute(key)
if ok {
val, err = goutils.InterfaceToBool(v)
@@ -259,7 +264,7 @@ func (s *BioSequence) MD5() [16]byte {
// Returning the number of times the sequence has been observed.
func (s *BioSequence) Count() int {
count, ok := s.GetInt("count")
count, ok := s.GetIntAttribute("count")
if !ok {
count = 1
@@ -270,7 +275,7 @@ func (s *BioSequence) Count() int {
// Returning the taxid of the sequence.
func (s *BioSequence) Taxid() int {
taxid, ok := s.GetInt("taxid")
taxid, ok := s.GetIntAttribute("taxid")
if !ok {
taxid = 1
@@ -330,6 +335,12 @@ func (s *BioSequence) WriteByteQualities(data byte) error {
return nil
}
// Clearing the sequence.
func (s *BioSequence) ClearQualities() {
s.qualities = s.qualities[0:0]
}
// A method that appends a byte slice to the sequence.
func (s *BioSequence) Write(data []byte) (int, error) {
s.sequence = append(s.sequence, data...)
@@ -347,3 +358,8 @@ func (s *BioSequence) WriteByte(data byte) error {
s.sequence = append(s.sequence, data)
return nil
}
// Clearing the sequence.
func (s *BioSequence) Clear() {
s.sequence = s.sequence[0:0]
}