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MarkDuplicates flow options now start with FLOW_ #1976

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Sep 10, 2024
Merged

MarkDuplicates flow options now start with FLOW_ #1976

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8 changes: 4 additions & 4 deletions src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowArgumentCollection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,21 +21,21 @@ public enum FLOW_DUPLICATE_SELECTION_STRATEGY {
"in addition to the start location, which is always significant (i.e. require single-ended reads to start and" +
"end on the same position to be considered duplicate) " +
"(for this argument, \"read end\" means 3' end).", optional = true)
public boolean USE_END_IN_UNPAIRED_READS = false;
public boolean FLOW_USE_END_IN_UNPAIRED_READS = false;

@Argument(doc = "Use position of the clipping as the end position, when considering duplicates (or use the unclipped end position) " +
"(for this argument, \"read end\" means 3' end).", optional = true)
public boolean USE_UNPAIRED_CLIPPED_END = false;
public boolean FLOW_USE_UNPAIRED_CLIPPED_END = false;

@Argument(doc = "Maximal difference of the read end position that counted as equal. Useful for flow based " +
"reads where the end position might vary due to sequencing errors. " +
"(for this argument, \"read end\" means 3' end)", optional = true)
public int UNPAIRED_END_UNCERTAINTY = 0;
public int FLOW_UNPAIRED_END_UNCERTAINTY = 0;

@Argument(doc = "Maximal difference of the read start position that counted as equal. Useful for flow based " +
"reads where the end position might vary due to sequencing errors. " +
"(for this argument, \"read start\" means 5' end in the direction of sequencing)", optional = true)
public int UNPAIRED_START_UNCERTAINTY = 0;
public int FLOW_UNPAIRED_START_UNCERTAINTY = 0;

@Argument(doc = "Skip first N flows, starting from the read's start, when considering duplicates. Useful for flow based reads where sometimes there " +
"is noise in the first flows " +
Expand Down
12 changes: 6 additions & 6 deletions src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
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Expand Up @@ -71,7 +71,7 @@ public MarkDuplicatesForFlowHelper(final MarkDuplicates md) {
}

private void validateFlowParameteres() {
if ( md.flowBasedArguments.UNPAIRED_END_UNCERTAINTY != 0 && !md.flowBasedArguments.USE_END_IN_UNPAIRED_READS ) {
if ( md.flowBasedArguments.FLOW_UNPAIRED_END_UNCERTAINTY != 0 && !md.flowBasedArguments.FLOW_USE_END_IN_UNPAIRED_READS) {
throw new IllegalArgumentException("Invalid parameter combination. UNPAIRED_END_UNCERTAINTY can not be specified when USE_END_IN_UNPAIRED_READS not specified");
}
}
Expand Down Expand Up @@ -175,7 +175,7 @@ public ReadEndsForMarkDuplicates buildReadEnds(final SAMFileHeader header, final

// adjust start/end coordinates
ends.read1Coordinate = getReadEndCoordinate(rec, !rec.getReadNegativeStrandFlag(), true, md.flowBasedArguments);
if (md.flowBasedArguments.USE_END_IN_UNPAIRED_READS) {
if (md.flowBasedArguments.FLOW_USE_END_IN_UNPAIRED_READS) {
ends.read2Coordinate = getReadEndCoordinate(rec, rec.getReadNegativeStrandFlag(), false, md.flowBasedArguments);
}

Expand Down Expand Up @@ -235,12 +235,12 @@ private boolean areComparableForDuplicatesWithEndSignificance(final ReadEndsForM

if (areComparable) {
areComparable = endCoorInRangeWithUncertainty(lhsRead1Coordinate1Min, lhsRead1Coordinate1Max,
rhs.read1Coordinate, md.flowBasedArguments.UNPAIRED_START_UNCERTAINTY);
rhs.read1Coordinate, md.flowBasedArguments.FLOW_UNPAIRED_START_UNCERTAINTY);
}
if (areComparable) {
areComparable = (!endCoorSignificant(lhs.read2Coordinate, rhs.read2Coordinate) ||
endCoorInRangeWithUncertainty(lhsRead1Coordinate2Min, lhsRead1Coordinate2Max,
rhs.read2Coordinate, md.flowBasedArguments.UNPAIRED_END_UNCERTAINTY));
rhs.read2Coordinate, md.flowBasedArguments.FLOW_UNPAIRED_END_UNCERTAINTY));
}

return areComparable;
Expand Down Expand Up @@ -377,7 +377,7 @@ protected static int getReadEndCoordinate(final SAMRecord rec, final boolean sta
if ( flowOrder.isValid() ) {

// simple case
if ( flowBasedArguments.USE_UNPAIRED_CLIPPED_END ) {
if ( flowBasedArguments.FLOW_USE_UNPAIRED_CLIPPED_END) {
return alignmentCoor;
}

Expand Down Expand Up @@ -412,7 +412,7 @@ protected static int getReadEndCoordinate(final SAMRecord rec, final boolean sta
}
}
final int coor = unclippedCoor + (startEnd ? hmerSize : -hmerSize);
return flowBasedArguments.USE_UNPAIRED_CLIPPED_END
return flowBasedArguments.FLOW_USE_UNPAIRED_CLIPPED_END
? (startEnd ? Math.max(coor, alignmentCoor) : Math.min(coor, alignmentCoor))
: coor;
}
Expand Down
28 changes: 14 additions & 14 deletions src/test/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelperTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12, null, false, null, null),
new TestRecordInfo(74, 12, null, true, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=false" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=false" }, null
},

// testUSE_END_IN_UNPAIRED_READS: End location is significant
Expand All @@ -96,7 +96,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12, null, false, null, null),
new TestRecordInfo(74, 12, null, false, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=true" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true" }, null
},

// testUSE_UNPAIRED_CLIPPED_END: Do not use clipped locations (meaning, use unclipped)
Expand All @@ -106,7 +106,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12, "1S76M", false, null, null),
new TestRecordInfo(74, 12, "74M", false, null, null)
},
new String[] { "USE_UNPAIRED_CLIPPED_END=false" }, null
new String[] { "FLOW_USE_UNPAIRED_CLIPPED_END=false" }, null
},

// testUSE_UNPAIRED_CLIPPED_END: Use clipped locations (meaning, use clipped)
Expand All @@ -116,7 +116,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12, "1S76M", false, null, null),
new TestRecordInfo(74, 12, "74M", true, null, null)
},
new String[] { "USE_UNPAIRED_CLIPPED_END=true" }, null
new String[] { "FLOW_USE_UNPAIRED_CLIPPED_END=true" }, null
},

// testUSE_UNPAIRED_CLIPPED_END: Use clipped locations (meaning, use clipped)
Expand All @@ -126,7 +126,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12, "1S76M1S", true, null, null),
new TestRecordInfo(78, 11, "78M", false, null, null)
},
new String[] { "USE_UNPAIRED_CLIPPED_END=false", "USE_END_IN_UNPAIRED_READS=true" }, null
new String[] { "FLOW_USE_UNPAIRED_CLIPPED_END=false", "FLOW_USE_END_IN_UNPAIRED_READS=true" }, null
},

// testUSE_UNPAIRED_CLIPPED_END: Use clipped locations (meaning, use clipped)
Expand All @@ -136,7 +136,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12, "1S76M1S", false, null, null),
new TestRecordInfo(78, 11, "78M", false, null, null)
},
new String[] { "USE_UNPAIRED_CLIPPED_END=true", "USE_END_IN_UNPAIRED_READS=true" }, null
new String[] { "FLOW_USE_UNPAIRED_CLIPPED_END=true", "FLOW_USE_END_IN_UNPAIRED_READS=true" }, null
},

// testFLOW_SKIP_FIRST_N_FLOWS: Do not use clipped locations (meaning, use unclipped)
Expand All @@ -146,7 +146,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12,"76M", false, "ACGTT", "TTGCA"),
new TestRecordInfo(76, 12, "76M", true, "ACGGT", "TGGCA")
},
new String[] { "USE_END_IN_UNPAIRED_READS=true", "FLOW_SKIP_FIRST_N_FLOWS=0" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true", "FLOW_SKIP_FIRST_N_FLOWS=0" }, null
},

// testFLOW_SKIP_FIRST_N_FLOWS: Do not use clipped locations (meaning, use unclipped)
Expand All @@ -156,7 +156,7 @@ public Object[][] forFlowDataProvider() {
new TestRecordInfo(76, 12,"76M", false, "ACGTT", "TTGCA"),
new TestRecordInfo(76, 12, "76M", false, "CCGGT", "TGGCA")
},
new String[] { "USE_END_IN_UNPAIRED_READS=true", "FLOW_SKIP_FIRST_N_FLOWS=3" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true", "FLOW_SKIP_FIRST_N_FLOWS=3" }, null
},

// testFLOW_QUALITY_SUM_STRATEGY: normal sum
Expand Down Expand Up @@ -226,7 +226,7 @@ public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester)
new TestRecordInfo(84, 12, null, true, null, null),
new TestRecordInfo(94, 12, null, false, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=true", "UNPAIRED_END_UNCERTAINTY=10" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true", "FLOW_UNPAIRED_END_UNCERTAINTY=10" }, null
},

// testUNPAIRED_START_UNCERTAINTY: End location is significant and uncertain, end sorted
Expand All @@ -237,7 +237,7 @@ public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester)
new TestRecordInfo(64, 22, null, true, null, null),
new TestRecordInfo(54, 32, null, true, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=true", "UNPAIRED_START_UNCERTAINTY=10" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true", "FLOW_UNPAIRED_START_UNCERTAINTY=10" }, null
},

// testUNPAIRED_END_UNCERTAINTY: End location is significant and uncertain, end not sorted
Expand All @@ -248,7 +248,7 @@ public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester)
new TestRecordInfo(194, 12, null, false, null, null),
new TestRecordInfo(184, 12, null, true, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=true", "UNPAIRED_END_UNCERTAINTY=10" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true", "FLOW_UNPAIRED_END_UNCERTAINTY=10" }, null
},

// testUNPAIRED_END_UNCERTAINTY: End location is significant and uncertain, end not sorted, multiple non-dup
Expand All @@ -259,7 +259,7 @@ public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester)
new TestRecordInfo(294, 12, null, false, null, null),
new TestRecordInfo(184, 12, null, false, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=true", "UNPAIRED_END_UNCERTAINTY=10" }, null
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=true", "FLOW_UNPAIRED_END_UNCERTAINTY=10" }, null
},
// Barcode
{
Expand All @@ -268,7 +268,7 @@ public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester)
new TestRecordInfo(76, 12, null, false, null, null),
new TestRecordInfo(74, 12, null, true, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=false", "BARCODE_TAG=BC" },
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=false", "BARCODE_TAG=BC" },
new TesterModifier() {
@Override
public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester) {
Expand All @@ -285,7 +285,7 @@ public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester)
new TestRecordInfo(76, 12, null, false, null, null),
new TestRecordInfo(74, 12, null, false, null, null)
},
new String[] { "USE_END_IN_UNPAIRED_READS=false", "BARCODE_TAG=BC" },
new String[] { "FLOW_USE_END_IN_UNPAIRED_READS=false", "BARCODE_TAG=BC" },
new TesterModifier() {
@Override
public void modify(final AbstractMarkDuplicatesCommandLineProgramTester tester) {
Expand Down
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