EpiProReadsReader (SMRT View)

java.lang.Object
- com.pacbio.secondary.vis.data.base.BaseDataModel
- - com.pacbio.secondary.vis.io.epipro.EpiProReadsReader

```
public class EpiProReadsReader
extends BaseDataModel
```
read subreadLength prologSubreadStart prologSubreadEnd prologRefid prologTstrand prologStart prologEnd prologScore prologPctsimilarity prologMapqv primarySubreadStart primarySubreadEnd primaryRefid primaryTstrand primaryStart primaryEnd primaryScore primaryPctsimilarity primaryMapqv epilogSubreadStart epilogSubreadEnd epilogRefid epilogTstrand epilogStart epilogEnd epilogScore epilogPctsimilarity epilogMapqv Are subread start/end coordinates in any way associated with strand? m130131_012042_42161_c100427120310000001523055601121430_s1_p0/664/14142_16905 2763 3 1316 ctg7180000000004 1 2234780 2233515 -5558 91.4371 254 1317 2763 ctg7180000000004 0 2233373 2234779 -6216 91.9137 254 _ _ _ _ _ _ _ _ _ Here looks like both epilog and prolog are located before primary segment. Is that expected, or is there is some strand-specific translation I should use? m130131_012042_42161_c100427120310000001523055601121430_s1_p0/1684/4359_11425 7066 5 288 ctg7180000000004 1 81994 81753 -939 82.8671 254 735 6289 ctg7180000000004 0 66386 70881 -15919 78.4593 254 241 300 ctg7180000000004 0 71057 71107 -205 84.7458 m130131_012042_42161_c100427120310000001523055601121430_s1_p0/4547/0_8798 8798 _ _ _ _ _ _ _ _ _ 9 8784 ctg7180000000004 1 4682440 4674672 -30326 83.9759 254 _ _ _ _ _ _ _ _ _ m130131_012042_42161_c100427120310000001523055601121430_s1_p0/1038/0_5417 5417 _ _ _ _ _ _ _ _ _ 14 2796 ctg7180000000004 1 484321 481659 -11763 91.4437 254 4 2614 ctg7180000000004 0 481825 484318 -10786 90.4833 254 m130131_012042_42161_c100427120310000001523055601121430_s1_p0/1892/0_13315 13315 _ _ _ _ _ _ _ _ _ 15 13298 ctg7180000000004 0 4603798 4616125 -50859 87.4192 254 _ _ _ _ _ _ _ _ _ m130131_012042_42161_c100427120310000001523055601121430_s1_p0/3639/0_6371 6371 _ _ _ _ _ _ _ _ _ 12 6371 ctg7180000000004 0 2045076 2051045 -25195 88.8838 254 _ _ _ _ _ _ _ _ _ m130131_012042_42161_c100427120310000001523055601121430_s1_p0/14/5198_6455 1257 _ _ _ _ _ _ _ _ _ 0 1246 ctg7180000000004 0 480066 481266 -4982 88.751 254 _ _ _ _ _ _ _ _ _ m130131_012042_42161_c100427120310000001523055601121430_s1_p0/1429/5424_7763 2339 _ _ _ _ _ _ _ _ _ 1 2331 ctg7180000000004 1 607406 605163 -8385 84.3865 254 _ _ _ _ _ _ _ _ _ m130131_012042_42161_c100427120310000001523055601121430_s1_p0/527/2181_4311 2130 _ _ _ _ _ _ _ _ _ 52 2127 ctg7180000000004 0 2459065 2461126 -8531 89.4058 254 _ _ _ _ _ _ _ _ _ m130131_012042_42161_c100427120310000001523055601121430_s1_p0/1564/4594_5659 1065 _ _ _ _ _ _ _ _ _ 0 1064 ctg7180000000004 1 3921712 3920730 -4089 87.6725 254 _ _ _ _ _ _ _ _ _ m130129_055833_42161_c100429140310000001523056601121482_s1_p0/43651/0_2316 2316 57 187 ctg7180000000006 1 48901 48793 -330 75.188 0 544 2310 ctg7180000000006 1 20857 19328 -5458 80.2537 0 _ _ _ _ _ _ _ _ _ m130129_010818_42161_c100429140310000001523056601121480_s1_p0/23928/0_7454 7454 _ _ _ _ _ _ _ _ _ 15 7383 ctg7180000000005 1 6893 -1 -28711 88.0524 0 _ _ _ _ _ _ _ _ _

Nested Class Summary
- Nested classes/interfaces inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel
  BaseDataModel.eDataType

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`abs_max_coverage`
`protected java.util.Vector<java.lang.String>`	`contig_full_names`
`protected java.util.Vector<java.lang.String>`	`contig_ids`
`protected java.util.Vector<java.lang.String>`	`contig_names`
`protected ContigInfo[]`	`contigs_info`
`protected static int`	`LANE_EXTRA_DISTANCE`
`protected static int`	`MAPPED_COORD_CORRECTION`
`protected int[]`	`max_lane`
`protected static int`	`MAX_ORDINATE_PILEUP`
`protected static int`	`MIN_LINES_FOR_DATA_HEAVY`
`protected static java.lang.String`	`SUBREAD_COUNT`
`protected int`	`UM_EPILOG_END`
`protected int`	`UM_EPILOG_MAPQV`
`protected int`	`UM_EPILOG_PCT_SIMILARITY`
`protected int`	`UM_EPILOG_REF_ID`
`protected int`	`UM_EPILOG_SCORE`
`protected int`	`UM_EPILOG_START`
`protected int`	`UM_EPILOG_STRAND`
`protected int`	`UM_EPILOG_SUBREAD_END`
`protected int`	`UM_EPILOG_SUBREAD_START`
`protected static java.lang.String`	`UM_NO_DATA`
`protected int`	`UM_PRIMARY_END`
`protected int`	`UM_PRIMARY_MAPQV`
`protected int`	`UM_PRIMARY_PCT_SIMILARITY`
`protected int`	`UM_PRIMARY_REF_ID`
`protected int`	`UM_PRIMARY_SCORE`
`protected int`	`UM_PRIMARY_START`
`protected int`	`UM_PRIMARY_STRAND`
`protected int`	`UM_PRIMARY_SUBREAD_END`
`protected int`	`UM_PRIMARY_SUBREAD_START`
`protected int`	`UM_PROLOG_END`
`protected int`	`UM_PROLOG_MAPQV`
`protected int`	`UM_PROLOG_PCT_SIMILARITY`
`protected int`	`UM_PROLOG_REF_ID`
`protected int`	`UM_PROLOG_SCORE`
`protected int`	`UM_PROLOG_START`
`protected int`	`UM_PROLOG_STRAND`
`protected int`	`UM_PROLOG_SUBREAD_END`
`protected int`	`UM_PROLOG_SUBREAD_START`
`protected int`	`UM_READ_ID`
`protected int`	`UM_SBR_LENGTH`
`protected java.lang.String`	`UM_SEPARATOR`
`protected int`	`UM_TOTAL_COLUMNS`
`protected int`	`use_epipro_mode`
`protected boolean`	`use_epipro_only`

Fields inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel
changeNotifier, data_type, mc

Constructor Summary

Constructors
Constructor and Description

EpiProReadsReader()

Constructors
Constructor and Description
`EpiProReadsReader()`

Method Summary

Methods
Modifier and Type	Method and Description
`protected void`	`assembleResultsWithoutStructures(java.util.ArrayList<Marker> alignedReads, int num_contigs)`
`void`	`clear()`
`protected int`	`getContigIndex(java.lang.String contig)`
`int`	`getMaxLane(int contig)`
`protected void`	`initContigInfo(VioletApp app)`
`void`	`loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)`
`protected int`	`PileUpContigResultsWithoutStructure(java.util.List<Marker> alignedReads)`
`protected Marker`	`processReadRecord(VioletApp app, java.lang.String[] ar, int contig_idx)`
`protected Marker`	`processSplitReadRecord(java.util.TreeMap<java.lang.Integer,java.lang.Integer> contigs_map, java.util.ArrayList<Marker> markers, java.lang.String[] ar, int contig_idx)`
`void`	`readElements(VioletApp app, java.io.Reader reader)`
`protected void`	`removeDataAboveThreshold()` eventually remove reads and structures with lane above max coverage threshold
`protected void`	`resetContigInfo()`
`protected void`	`UpdateProgressBar(VioletApp app, double pct)`

Methods inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel
addChangeListener, fireChangeEvent, getDataType, getDataTypeAsString, getMarkersForContig, getNumContigs, hasData, isMarkerType, isModificationsType, isReadsType, isSummaryType, isVariantsType, removeChangeListener, setTypeAndNumContigs

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- MAPPED_COORD_CORRECTION
```
protected static final int MAPPED_COORD_CORRECTION
```
  See Also:
  Constant Field Values
- MAX_ORDINATE_PILEUP
```
protected static final int MAX_ORDINATE_PILEUP
```
  See Also:
  Constant Field Values
- LANE_EXTRA_DISTANCE
```
protected static final int LANE_EXTRA_DISTANCE
```
  See Also:
  Constant Field Values
- SUBREAD_COUNT
```
protected static final java.lang.String SUBREAD_COUNT
```
  See Also:
  Constant Field Values
- MIN_LINES_FOR_DATA_HEAVY
```
protected static int MIN_LINES_FOR_DATA_HEAVY
```
- UM_SEPARATOR
```
protected final java.lang.String UM_SEPARATOR
```
  See Also:
  Constant Field Values
- UM_READ_ID
```
protected final int UM_READ_ID
```
  See Also:
  Constant Field Values
- UM_SBR_LENGTH
```
protected final int UM_SBR_LENGTH
```
  See Also:
  Constant Field Values
- UM_PROLOG_SUBREAD_START
```
protected final int UM_PROLOG_SUBREAD_START
```
  See Also:
  Constant Field Values
- UM_PROLOG_SUBREAD_END
```
protected final int UM_PROLOG_SUBREAD_END
```
  See Also:
  Constant Field Values
- UM_PROLOG_REF_ID
```
protected final int UM_PROLOG_REF_ID
```
  See Also:
  Constant Field Values
- UM_PROLOG_STRAND
```
protected final int UM_PROLOG_STRAND
```
  See Also:
  Constant Field Values
- UM_PROLOG_START
```
protected final int UM_PROLOG_START
```
  See Also:
  Constant Field Values
- UM_PROLOG_END
```
protected final int UM_PROLOG_END
```
  See Also:
  Constant Field Values
- UM_PROLOG_SCORE
```
protected final int UM_PROLOG_SCORE
```
  See Also:
  Constant Field Values
- UM_PROLOG_PCT_SIMILARITY
```
protected final int UM_PROLOG_PCT_SIMILARITY
```
  See Also:
  Constant Field Values
- UM_PROLOG_MAPQV
```
protected final int UM_PROLOG_MAPQV
```
  See Also:
  Constant Field Values
- UM_PRIMARY_SUBREAD_START
```
protected final int UM_PRIMARY_SUBREAD_START
```
  See Also:
  Constant Field Values
- UM_PRIMARY_SUBREAD_END
```
protected final int UM_PRIMARY_SUBREAD_END
```
  See Also:
  Constant Field Values
- UM_PRIMARY_REF_ID
```
protected final int UM_PRIMARY_REF_ID
```
  See Also:
  Constant Field Values
- UM_PRIMARY_STRAND
```
protected final int UM_PRIMARY_STRAND
```
  See Also:
  Constant Field Values
- UM_PRIMARY_START
```
protected final int UM_PRIMARY_START
```
  See Also:
  Constant Field Values
- UM_PRIMARY_END
```
protected final int UM_PRIMARY_END
```
  See Also:
  Constant Field Values
- UM_PRIMARY_SCORE
```
protected final int UM_PRIMARY_SCORE
```
  See Also:
  Constant Field Values
- UM_PRIMARY_PCT_SIMILARITY
```
protected final int UM_PRIMARY_PCT_SIMILARITY
```
  See Also:
  Constant Field Values
- UM_PRIMARY_MAPQV
```
protected final int UM_PRIMARY_MAPQV
```
  See Also:
  Constant Field Values
- UM_EPILOG_SUBREAD_START
```
protected final int UM_EPILOG_SUBREAD_START
```
  See Also:
  Constant Field Values
- UM_EPILOG_SUBREAD_END
```
protected final int UM_EPILOG_SUBREAD_END
```
  See Also:
  Constant Field Values
- UM_EPILOG_REF_ID
```
protected final int UM_EPILOG_REF_ID
```
  See Also:
  Constant Field Values
- UM_EPILOG_STRAND
```
protected final int UM_EPILOG_STRAND
```
  See Also:
  Constant Field Values
- UM_EPILOG_START
```
protected final int UM_EPILOG_START
```
  See Also:
  Constant Field Values
- UM_EPILOG_END
```
protected final int UM_EPILOG_END
```
  See Also:
  Constant Field Values
- UM_EPILOG_SCORE
```
protected final int UM_EPILOG_SCORE
```
  See Also:
  Constant Field Values
- UM_EPILOG_PCT_SIMILARITY
```
protected final int UM_EPILOG_PCT_SIMILARITY
```
  See Also:
  Constant Field Values
- UM_EPILOG_MAPQV
```
protected final int UM_EPILOG_MAPQV
```
  See Also:
  Constant Field Values
- UM_TOTAL_COLUMNS
```
protected final int UM_TOTAL_COLUMNS
```
  See Also:
  Constant Field Values
- UM_NO_DATA
```
protected static final java.lang.String UM_NO_DATA
```
  See Also:
  Constant Field Values
- abs_max_coverage
```
protected int abs_max_coverage
```
- use_epipro_only
```
protected boolean use_epipro_only
```
- use_epipro_mode
```
protected int use_epipro_mode
```
- max_lane
```
protected int[] max_lane
```
- contigs_info
```
protected ContigInfo[] contigs_info
```
- contig_ids
```
protected java.util.Vector<java.lang.String> contig_ids
```
- contig_names
```
protected java.util.Vector<java.lang.String> contig_names
```
- contig_full_names
```
protected java.util.Vector<java.lang.String> contig_full_names
```

Constructor Detail
- EpiProReadsReader
```
public EpiProReadsReader()
```

Method Detail

getMaxLane
```
public int getMaxLane(int contig)
```

initContigInfo

protected void initContigInfo(VioletApp app)

resetContigInfo
```
protected void resetContigInfo()
```

loadFromReader

public void loadFromReader(java.io.Reader reader,
                  java.lang.String file_name,
                  VioletApp app)
                    throws java.io.IOException,
                           FileFormatException

Throws:: java.io.IOException; FileFormatException

getContigIndex

protected int getContigIndex(java.lang.String contig)

readElements

public void readElements(VioletApp app,
                java.io.Reader reader)
                  throws java.io.IOException,
                         FileFormatException

Throws:: java.io.IOException; FileFormatException

UpdateProgressBar

protected void UpdateProgressBar(VioletApp app,
                     double pct)

processReadRecord

protected Marker processReadRecord(VioletApp app,
                       java.lang.String[] ar,
                       int contig_idx)

Parameters:: ar -; contig_idx -
Returns:

processSplitReadRecord

protected Marker processSplitReadRecord(java.util.TreeMap<java.lang.Integer,java.lang.Integer> contigs_map,
                            java.util.ArrayList<Marker> markers,
                            java.lang.String[] ar,
                            int contig_idx)

Parameters:: ar -; contig_idx -
Returns:

assembleResultsWithoutStructures

protected void assembleResultsWithoutStructures(java.util.ArrayList<Marker> alignedReads,
                                    int num_contigs)

PileUpContigResultsWithoutStructure

protected int PileUpContigResultsWithoutStructure(java.util.List<Marker> alignedReads)

removeDataAboveThreshold
```
protected void removeDataAboveThreshold()
```
eventually remove reads and structures with lane above max coverage threshold

Parameters:
results -
alignedReads -
mode -

clear
```
public void clear()
```

Class EpiProReadsReader

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

Field Summary

Fields inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

Constructor Summary

Method Summary

Methods inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

Methods inherited from class java.lang.Object

Field Detail

MAPPED_COORD_CORRECTION

MAX_ORDINATE_PILEUP

LANE_EXTRA_DISTANCE

SUBREAD_COUNT

MIN_LINES_FOR_DATA_HEAVY

UM_SEPARATOR

UM_READ_ID

UM_SBR_LENGTH

UM_PROLOG_SUBREAD_START

UM_PROLOG_SUBREAD_END

UM_PROLOG_REF_ID

UM_PROLOG_STRAND

UM_PROLOG_START

UM_PROLOG_END

UM_PROLOG_SCORE

UM_PROLOG_PCT_SIMILARITY

UM_PROLOG_MAPQV

UM_PRIMARY_SUBREAD_START

UM_PRIMARY_SUBREAD_END

UM_PRIMARY_REF_ID

UM_PRIMARY_STRAND

UM_PRIMARY_START

UM_PRIMARY_END

UM_PRIMARY_SCORE

UM_PRIMARY_PCT_SIMILARITY

UM_PRIMARY_MAPQV

UM_EPILOG_SUBREAD_START

UM_EPILOG_SUBREAD_END

UM_EPILOG_REF_ID

UM_EPILOG_STRAND

UM_EPILOG_START

UM_EPILOG_END

UM_EPILOG_SCORE

UM_EPILOG_PCT_SIMILARITY

UM_EPILOG_MAPQV

UM_TOTAL_COLUMNS

UM_NO_DATA

abs_max_coverage

use_epipro_only

use_epipro_mode

max_lane

contigs_info

contig_ids

contig_names

contig_full_names

Constructor Detail

EpiProReadsReader

Method Detail

getMaxLane

initContigInfo

resetContigInfo

loadFromReader

getContigIndex

readElements

UpdateProgressBar

processReadRecord

processSplitReadRecord

assembleResultsWithoutStructures

PileUpContigResultsWithoutStructure

removeDataAboveThreshold

clear