BamWriter

Constructors

this

this(contrib.undead.stream.Stream stream, int compression_level, std.parallelism.TaskPool task_pool, size_t buffer_size)

this(string filename, int compression_level, std.parallelism.TaskPool task_pool)

Creates new BAM writer outputting to file or stream. Automatically writes BAM magic number (4 bytes).

Members

Functions

disableAutoIndexCreation

void disableAutoIndexCreation()

By default, the writer attempts to automatically create index when writing coordinate-sorted files. If this behaviour is not desired, it can be switched off before writing SAM header.

finish

void finish()

Flushes buffer and closes output stream. Adds BAM EOF block automatically.

flush

void flush()

Flushes current BGZF block.

setFilename

void setFilename(string output_filename)

Can be called right after the stream constructor, only once

writeByteArray

void writeByteArray(const(ubyte[]) array)

Undocumented in source. Be warned that the author may not have intended to support it.

writeInteger

void writeInteger(T integer)

Undocumented in source. Be warned that the author may not have intended to support it.

writeRecord

void writeRecord(R read)

Writes BAM read. Throws exception if read reference ID is out of range.

writeReferenceSequenceInfo

void writeReferenceSequenceInfo(const(bio.std.hts.bam.referenceinfo.ReferenceSequenceInfo)[] reference_sequences)

Writes reference sequence information. Should be called after dumping SAM header. Writer will store this array to use later for resolving read reference IDs to names.

writeSamHeader

void writeSamHeader(bio.std.hts.sam.header.SamHeader header)

void writeSamHeader(string header_text)

Writes SAM header. Should be called after construction.

writeString

void writeString(string str)

Undocumented in source. Be warned that the author may not have intended to support it.

import bio.std.hts.bam.writer, bio.std.hts.bam.reader;
...
auto src = new BamReader("in.bam");
auto dst = new BamWriter("out.bam", 9); // maximal compression
scope (exit) dst.finish();              // close the stream at exit
dst.writeSamHeader(src.header);         // copy header and reference sequence info
dst.writeReferenceSequenceInfo(src.reference_sequences);
foreach (read; src.reads) {
    if (read.mapping_quality > 10)      // skip low-quality reads
        dst.writeRecord(read);
}

• BamWriter