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Add ncbi version aliasing, .x -> no version
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133 changes: 133 additions & 0 deletions
133
src/main/java/org/broad/igv/sam/EmptyAlignmentCounts.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,133 @@ | ||
| package org.broad.igv.sam; | ||
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| public class EmptyAlignmentCounts implements AlignmentCounts { | ||
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| private static EmptyAlignmentCounts instance; | ||
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| public static AlignmentCounts getInstance() { | ||
| if(instance == null) { | ||
| instance = new EmptyAlignmentCounts(); | ||
| } | ||
| return instance; | ||
| } | ||
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| @Override | ||
| public void incCounts(Alignment alignment) { | ||
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| } | ||
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| @Override | ||
| public int getTotalCount(int pos) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getTotalPositiveCount(int pos) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getTotalNegativeCount(int pos) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getTotalQuality(int pos) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getCount(int pos, byte b) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getNegCount(int pos, byte b) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getPosCount(int pos, byte b) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getDelCount(int pos) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getInsCount(int pos) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getQuality(int pos, byte b) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getNumberOfPoints() { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getMaxCount(int origin, int end) { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public String getValueStringAt(int pos) { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public boolean isConsensusMismatch(int pos, byte ref, String chr, float snpThreshold) { | ||
| return false; | ||
| } | ||
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| @Override | ||
| public boolean isConsensusDeletion(int start, int end, float snpThreshold) { | ||
| return false; | ||
| } | ||
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| @Override | ||
| public boolean isConsensusInsertion(int pos, float snpThreshold) { | ||
| return false; | ||
| } | ||
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| @Override | ||
| public BisulfiteCounts getBisulfiteCounts() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public int getBucketSize() { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public boolean hasBaseCounts() { | ||
| return false; | ||
| } | ||
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| @Override | ||
| public void finish() { | ||
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| } | ||
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| @Override | ||
| public String getContig() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public int getStart() { | ||
| return 0; | ||
| } | ||
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| @Override | ||
| public int getEnd() { | ||
| return 0; | ||
| } | ||
| } |
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