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bgzf-check.go
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bgzf-check.go
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// elPrep: a high-performance tool for analyzing SAM/BAM files.
// Copyright (c) 2017-2020 imec vzw.
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU Affero General Public License as
// published by the Free Software Foundation, either version 3 of the
// License, or (at your option) any later version, and Additional Terms
// (see below).
// This program is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Affero General Public License for more details.
// You should have received a copy of the GNU Affero General Public
// License and Additional Terms along with this program. If not, see
// <https://github.com/ExaScience/elprep/blob/master/LICENSE.txt>.
package utils
import (
"bufio"
"io"
"log"
"github.com/exascience/elprep/v5/utils/bgzf"
)
// HandleBGZF checks if the given reader produces a gzip file
// by looking at the initial byte. It then either returns
// a bgzf.Reader, or returns the given reader unchanged.
// HandleBGZF uses ReadByte und UnreadByte.
func HandleBGZF(buf *bufio.Reader) io.Reader {
if ok, err := bgzf.IsGzip(buf); err != nil {
log.Panic(err)
return nil
} else if ok {
if r, err := bgzf.NewReader(buf); err != nil {
log.Panic(err)
return nil
} else {
return r
}
} else {
return buf
}
}