Filter bam reads. More...
#include <yat/omic/BamReadFilter.h>
Inheritance diagram for theplu::yat::omic::BamReadFilter:
Public Member Functions | |
| BamReadFilter (unsigned char mapQ, unsigned int filtered_flags=BAM_DEF_MASK, unsigned int required_flags=0) | |
| bool | operator() (const BamRead &bam) const |
Detailed Description
Filter bam reads.
Class is specifically designed to be used with boost::filter_iterator. The code below for example
InBamFile in("example.bam");
BamReadIterator begin(in);
BamReadIterator end;
BamReadFilter filter(20, 0);
some_algo(make_filter_iterator(filter, begin, end),
make_filter_iterator(filter, end));
iterates over all read with mapping quality 20 or greater.
- Since
- new in yat 0.11
Constructor & Destructor Documentation
| theplu::yat::omic::BamReadFilter::BamReadFilter | ( | unsigned char | mapQ, |
| unsigned int | filtered_flags = BAM_DEF_MASK, |
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| unsigned int | required_flags = 0 |
||
| ) |
Create a functor which accepts reads with mapping quality mapQ (or greater), flag must be unset in bits described by a filter_flags, and flag must be set in bits described by required_flags.
Member Function Documentation
| bool theplu::yat::omic::BamReadFilter::operator() | ( | const BamRead & | bam | ) | const |
return true if 1) bam mapping quality is at least mapQ AND 2) bam flags & filter_flags == 0 (no filter bit set) AND 3) bam flags & required_flags == required_flags (all req bits set)
The documentation for this class was generated from the following file:
- yat/omic/BamReadFilter.h
