Uses of Class
com.pacbio.secondary.vis.io.hdf.data.RawRead

Packages that use RawRead

Package	Description
com.pacbio.secondary.vis.io.hdf.file.cmph5	Support for reading/writing of cmp.h5 files
com.pacbio.secondary.vis.svc.server.hdf	HDFService utils

Uses of RawRead in com.pacbio.secondary.vis.io.hdf.file.cmph5

Methods in com.pacbio.secondary.vis.io.hdf.file.cmph5 that return RawRead

Modifier and Type	Method and Description
protected RawRead	CMPH5FileData.getSingleRawRead(AlignmentIndexTable table, int row_idx) Deprecated.
RawRead	CMPH5FileData.getSingleRawReadUsingCache(H5ScalarDS read_align_dataset, H5ScalarDS read_metrics_dataset, AlignmentIndexTable table, int row_idx)
RawRead	CMPH5FileData.updateSingleRawReadUsingCache(RawRead read, H5ScalarDS read_metrics_dataset, AlignmentIndexTable table, int row_idx)

Methods in com.pacbio.secondary.vis.io.hdf.file.cmph5 with parameters of type RawRead

Modifier and Type	Method and Description
RawRead	CMPH5FileData.updateSingleRawReadUsingCache(RawRead read, H5ScalarDS read_metrics_dataset, AlignmentIndexTable table, int row_idx)

Uses of RawRead in com.pacbio.secondary.vis.svc.server.hdf

Methods in com.pacbio.secondary.vis.svc.server.hdf that return types with arguments of type RawRead

Modifier and Type	Method and Description
protected java.util.ArrayList<RawRead>	GenomicDataBuilder.gatherBasesData(CMPH5File cmp_h5_file, java.util.ArrayList<WsRead> alignedReads, AlignmentIndexTable table, long start, long end, int mode)

Methods in com.pacbio.secondary.vis.svc.server.hdf with parameters of type RawRead

Modifier and Type	Method and Description
protected void	GenomicDataStructures.createFromRawRead(WsRead aligned_read, RawRead read_data, float metrics_factor, int mode) must report right or left insertion...
protected void	GenomicDataStructures.createFromRawReadWithInsertions(WsRead aligned_read, RawRead read_data, float metrics_factor, int mode, long start_from) report insertion at position...
protected void	GenomicDataStructures.reverseRawRead(RawRead read_data) handles reverse strand data
protected void	GenomicDataStructures.setQVValue(WsRead aligned_read, RawRead read_data, int raw_base_index, int annotated_base_index, float metrics_factor)
protected void	GenomicDataStructures.updateMetricsFromRawRead(WsRead aligned_read, RawRead read_data, float metrics_factor) must report right or left insertion...

Method parameters in com.pacbio.secondary.vis.svc.server.hdf with type arguments of type RawRead

Modifier and Type	Method and Description
protected WsResults	GenomicDataBuilder.copyResults(WsResults results, java.util.List<WsRead> alignedReads, java.util.List<RawRead> raw_reads, float metrics_factor, int mode) copy as basic array from arraylist
protected float	GenomicDataBuilder.gatherMetricsData(CMPH5File cmp_h5_file, java.util.ArrayList<WsRead> alignedReads, java.util.ArrayList<RawRead> raw_reads, AlignmentIndexTable table, long start, long end, int mode)