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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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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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6
pkg/obiformats/fastqseq_read.go
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@@ -17,7 +17,7 @@ import (
func EndOfLastFastqEntry(buffer []byte) int {
var i int
// log.Warnf("EndOfLastFastqEntry(%d): %s", len(buffer), string(buffer[0:20]))
// obilog.Warnf("EndOfLastFastqEntry(%d): %s", len(buffer), string(buffer[0:20]))
imax := len(buffer)
state := 0
restart := imax - 1
@@ -74,7 +74,7 @@ func EndOfLastFastqEntry(buffer []byte) int {
state = 3
} else {
// it was not the sequence part
// log.Warnf("it was not the sequence part : %c", C)
// obilog.Warnf("it was not the sequence part : %c", C)
state = 0
i = restart
}
@@ -101,7 +101,7 @@ func EndOfLastFastqEntry(buffer []byte) int {
// log.Warn("====> End of the last sequence")
state = 7
} else {
// log.Warnf("%s: Strange it was not the end of the last sequence : %c : %s", string(buffer[0:40]), C, string(buffer[i-20:i+5]))
// obilog.Warnf("%s: Strange it was not the end of the last sequence : %c : %s", string(buffer[0:40]), C, string(buffer[i-20:i+5]))
state = 5
}
}