com.pacbio.secondary.vis.svc.server.hdf

Class GenomicDataBuilder

java.lang.Object

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder

Direct Known Subclasses:

GenomicDataServer

public class GenomicDataBuilder
extends GenomicDataAssembler

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

GenomicDataStructures.WsReadStructure

Field Summary

Fields inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

CHIMERIC_STANDARD_THRESHOLD, CHIMERIC_STROBE_THRESHOLD, LANE_EXTRA_DISTANCE, MAX_ORDINATE_PILEUP

Fields inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

BASE_DELETION, BASE_LEFT_INSERTION, BASE_MATCH, BASE_POS_INSERTION, BASE_RIGHT_INSERTION, BASE_SVN

Constructor Summary

Constructors

Constructor and Description
GenomicDataBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
protected WsResults	assembleReads(WsResults results, int mode, java.util.List<WsRead> alignedReads, boolean isStrobe, boolean isV12, long start_time, int client_contig_index, long start, long end, long total_bases) analyze and pile-up reads, create structure info and results metadata
protected WsResults	copyResults(WsResults results, java.util.List<WsRead> alignedReads)
protected WsResults	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 java.util.ArrayList<RawRead>	gatherBasesData(CMPH5File cmp_h5_file, java.util.ArrayList<WsRead> alignedReads, AlignmentIndexTable table, long start, long end, int mode)
protected float	gatherMetricsData(CMPH5File cmp_h5_file, java.util.ArrayList<WsRead> alignedReads, java.util.ArrayList<RawRead> raw_reads, AlignmentIndexTable table, long start, long end, int mode)
protected WsResults	getReadsDataFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, int mode) getAlignedReadsFromFile
protected WsResults	getReadsDataWithInsertionsFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, int mode)
protected WsResults	prepareResults(WsResults results, int mode, java.util.ArrayList<WsRead> alignedReads, boolean isStrobe, boolean isV12, long start_time, int client_contig_index, long start, long end, long total_bases)
protected void	removeDataAboveThreshold(WsResults results, java.util.List<WsRead> alignedReads, int mode) eventually remove reads and structures with lane above max coverage threshold
protected void	updateIOTimeStats(WsResults results, long start_time)

Methods inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

assembleResultsWithoutStructures, assembleResultsWithStructures, createGraphLinesStructure, createGraphLinksStructure, createGraphNodesStructure, createGraphStructure, PileUpResultsWithoutStructure, PileUpResultsWithoutStructureForBaseMods, PileUpResultsWithStructures

Methods inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

buildStats, createFromRawRead, createFromRawReadWithInsertions, reverse, reverse, reverse, reverseRawRead, setQVValue, updateMetricsFromRawRead

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenomicDataBuilder

public GenomicDataBuilder()

Method Detail

getReadsDataFromFile

protected WsResults getReadsDataFromFile(java.lang.String url,
                             java.lang.String contig_id,
                             int client_contig_index,
                             long start,
                             long end,
                             int mode)

getAlignedReadsFromFile

Parameters:

url -

contig_id -

client_contig_index -

start -

end -

Returns:

copyResults

protected WsResults 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

Parameters:

results -

alignedReads -

Returns:

gatherBasesData

protected java.util.ArrayList<RawRead> gatherBasesData(CMPH5File cmp_h5_file,
                                           java.util.ArrayList<WsRead> alignedReads,
                                           AlignmentIndexTable table,
                                           long start,
                                           long end,
                                           int mode)

Parameters:

cmp_h5_file -

alignedReads -

table -

start -

end -

mode -

gatherMetricsData

protected float gatherMetricsData(CMPH5File cmp_h5_file,
                      java.util.ArrayList<WsRead> alignedReads,
                      java.util.ArrayList<RawRead> raw_reads,
                      AlignmentIndexTable table,
                      long start,
                      long end,
                      int mode)

Parameters:

cmp_h5_file -

alignedReads -

table -

start -

end -

mode -

prepareResults

protected WsResults prepareResults(WsResults results,
                       int mode,
                       java.util.ArrayList<WsRead> alignedReads,
                       boolean isStrobe,
                       boolean isV12,
                       long start_time,
                       int client_contig_index,
                       long start,
                       long end,
                       long total_bases)

Parameters:

results -

mode -

alignedReads -

isStrobe -

isV12 -

start_time -

client_contig_index -

start -

end -

total_bases -

assembleReads

protected WsResults assembleReads(WsResults results,
                      int mode,
                      java.util.List<WsRead> alignedReads,
                      boolean isStrobe,
                      boolean isV12,
                      long start_time,
                      int client_contig_index,
                      long start,
                      long end,
                      long total_bases)

analyze and pile-up reads, create structure info and results metadata

Parameters:

results -

mode -

alignedReads -

isStrobe -

isV12 -

start_time -

client_contig_index -

start -

end -

total_bases -

Returns:

removeDataAboveThreshold

protected void removeDataAboveThreshold(WsResults results,
                            java.util.List<WsRead> alignedReads,
                            int mode)

eventually remove reads and structures with lane above max coverage threshold

Parameters:

results -

alignedReads -

mode -

updateIOTimeStats

protected void updateIOTimeStats(WsResults results,
                     long start_time)

Parameters:

results -

start_time -

getReadsDataWithInsertionsFromFile

protected WsResults getReadsDataWithInsertionsFromFile(java.lang.String url,
                                           java.lang.String contig_id,
                                           int client_contig_index,
                                           long start,
                                           long end,
                                           int mode)

Parameters:

url -

contig_id -

client_contig_index -

start -

end -

mode -

Returns:

copyResults

protected WsResults copyResults(WsResults results,
                    java.util.List<WsRead> alignedReads)

Parameters:

results -

alignedReads -

Returns: