utility class to write out a SAM/BAM/CRAM file to any stream
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#include <sam_writer.h>
utility class to write out a SAM/BAM/CRAM file to any stream
- Todo:
- add serialization option
| gamgee::SamWriter::SamWriter |
( |
const std::string & |
output_fname = "-", |
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const bool |
binary = true |
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) |
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explicit |
Creates a new SamWriter using the specified output file name.
- Parameters
-
| output_fname | file to write to. The default is stdout (as defined by htslib) |
| binary | whether the output should be in BAM (true) or SAM format (false) |
- Note
- the header is copied and managed internally
| gamgee::SamWriter::SamWriter |
( |
const SamHeader & |
header, |
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const std::string & |
output_fname = "-", |
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const bool |
binary = true |
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) |
| |
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explicit |
Creates a new SamWriter with the header extracted from a Sam record and using the specified output file name.
- Parameters
-
| header | SamHeader object to make a copy from |
| output_fname | file to write to. The default is stdout (as defined by htslib) |
| binary | whether the output should be in BAM (true) or SAM format (false) |
- Note
- the header is copied and managed internally
| gamgee::SamWriter::SamWriter |
( |
const SamWriter & |
other | ) |
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delete |
a SamWriter cannot be copied safely, as it is iterating over a stream.
| gamgee::SamWriter::SamWriter |
( |
SamWriter && |
other | ) |
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default |
| void gamgee::SamWriter::add_header |
( |
const SamHeader & |
header | ) |
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Adds a header to the file stream.
- Parameters
-
- Note
- the header is a requirement to add records
| void gamgee::SamWriter::add_record |
( |
const Sam & |
body | ) |
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Adds a record to the file stream.
- Parameters
-
The documentation for this class was generated from the following files:
1.8.8