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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

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This commit is contained in:
Eric Coissac
2025-03-25 16:44:46 +01:00
parent 2ab6f67d58
commit 5a3705b6bb
52 changed files with 151 additions and 90 deletions
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24
pkg/obingslibrary/multimatch.go
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@ -87,7 +87,7 @@ func lookForTag(seq string, delimiter byte) string {
i := len(seq) - 1
// log.Warnf("Provided fragment : %s", string(seq))
// obilog.Warnf("Provided fragment : %s", string(seq))
for i >= 0 && seq[i] != delimiter {
i--
@ -109,7 +109,7 @@ func lookForTag(seq string, delimiter byte) string {
return ""
}
// log.Warnf("extracted : %s", string(seq[begin:end]))
// obilog.Warnf("extracted : %s", string(seq[begin:end]))
return seq[begin:end]
}
@ -340,8 +340,8 @@ func (marker *Marker) beginTagExtractor(
sequence *obiseq.BioSequence,
begin int,
forward bool) string {
// log.Warnf("Forward : %v -> %d %c", forward, marker.Forward_spacer, marker.Forward_tag_delimiter)
// log.Warnf("Forward : %v -> %d %c", forward, marker.Reverse_spacer, marker.Reverse_tag_delimiter)
// obilog.Warnf("Forward : %v -> %d %c", forward, marker.Forward_spacer, marker.Forward_tag_delimiter)
// obilog.Warnf("Forward : %v -> %d %c", forward, marker.Reverse_spacer, marker.Reverse_tag_delimiter)
if forward {
if marker.Forward_tag_length == 0 {
return ""
@ -351,10 +351,10 @@ func (marker *Marker) beginTagExtractor(
return marker.beginFixedTagExtractor(sequence, begin, forward)
} else {
if marker.Forward_tag_indels == 0 {
// log.Warnf("Delimited tag for forward primers %s", marker.forward.String())
// obilog.Warnf("Delimited tag for forward primers %s", marker.forward.String())
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
} else {
// log.Warnf("Rescue tag for forward primers %s", marker.forward.String())
// obilog.Warnf("Rescue tag for forward primers %s", marker.forward.String())
return marker.beginRescueTagExtractor(sequence, begin, forward)
}
}
@ -367,10 +367,10 @@ func (marker *Marker) beginTagExtractor(
return marker.beginFixedTagExtractor(sequence, begin, forward)
} else {
if marker.Reverse_tag_indels == 0 {
// log.Warnf("Delimited tag for reverse/complement primers %s", marker.creverse.String())
// obilog.Warnf("Delimited tag for reverse/complement primers %s", marker.creverse.String())
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
} else {
// log.Warnf("Rescue tag for reverse/complement primers %s", marker.creverse.String())
// obilog.Warnf("Rescue tag for reverse/complement primers %s", marker.creverse.String())
return marker.beginRescueTagExtractor(sequence, begin, forward)
}
}
@ -390,10 +390,10 @@ func (marker *Marker) endTagExtractor(
return marker.endFixedTagExtractor(sequence, end, forward)
} else {
if marker.Reverse_tag_indels == 0 {
// log.Warnf("Delimited tag for reverse primers %s", marker.reverse.String())
// obilog.Warnf("Delimited tag for reverse primers %s", marker.reverse.String())
return marker.endDelimitedTagExtractor(sequence, end, forward)
} else {
// log.Warnf("Rescue tag for reverse primers %s", marker.reverse.String())
// obilog.Warnf("Rescue tag for reverse primers %s", marker.reverse.String())
return marker.endRescueTagExtractor(sequence, end, forward)
}
}
@ -406,10 +406,10 @@ func (marker *Marker) endTagExtractor(
return marker.endFixedTagExtractor(sequence, end, forward)
} else {
if marker.Forward_tag_indels == 0 {
// log.Warnf("Delimited tag for forward/complement primers %s", marker.cforward.String())
// obilog.Warnf("Delimited tag for forward/complement primers %s", marker.cforward.String())
return marker.endDelimitedTagExtractor(sequence, end, forward)
} else {
// log.Warnf("Rescue tag for forward/complement primers %s", marker.cforward.String())
// obilog.Warnf("Rescue tag for forward/complement primers %s", marker.cforward.String())
return marker.endRescueTagExtractor(sequence, end, forward)
}
}