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

Packages that use AlignmentIndexTable

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 AlignmentIndexTable in com.pacbio.secondary.vis.io.hdf.file.cmph5

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

Modifier and Type	Method and Description
AlignmentIndexTable	CMPH5FileBase.getAlignmentIndexTableForContig(java.lang.String contig_id) Simple method to get cmp.h5 alignment index data for a specific contig.

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

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)

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

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

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)
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)