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Hotfix for various TagPileup bugs #77

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Merged
WilliamKMLai merged 4 commits into from
Jan 3, 2022
Merged

Hotfix for various TagPileup bugs #77

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a69d90a
fix TP Anti 1bp shift
owlang Dec 23, 2021
c3109d5
fix TP BEDcoord-strand shift
owlang Dec 23, 2021
b54b347
TP change insert size calculation
owlang Dec 24, 2021
0d300ec
reset default BED coord strand parsing
owlang Dec 24, 2021
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38 changes: 19 additions & 19 deletions src/scripts/Read_Analysis/PileupScripts/PileupExtract.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,11 +48,6 @@ public void extract(BEDCoord read) {

int BEDSTART = (int)read.getStart();
int BEDSTOP = (int)read.getStop();
//Correct for '-' strand BED coord so they align with '+' strand
if(read.getDir().equals("-")) {
BEDSTART++;
BEDSTOP++;
}

//Correct Window Size for proper transformations
int WINDOW = (BEDSTOP - BEDSTART) + ((param.getBin() / 2) * 2);
Expand Down Expand Up @@ -81,24 +76,29 @@ else if(param.getTrans() == 2) {
if((sr.getFirstOfPairFlag() && param.getRead() == 0) || (!sr.getFirstOfPairFlag() && param.getRead() == 1) || param.getRead() == 2 || (sr.getFirstOfPairFlag() && param.getRead() == 3)) {
int FivePrime = sr.getUnclippedStart() - 1;
if(sr.getReadNegativeStrandFlag()) {
FivePrime = sr.getUnclippedEnd();
FivePrime = sr.getUnclippedEnd() - 1;
FivePrime -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
} else { FivePrime += SHIFT; }

if(sr.getProperPairFlag()) { //prevent cases where non-properly paired Read1 gets to this point
int recordStart = sr.getUnclippedStart() - 1;
int recordStop = sr.getMateAlignmentStart() + sr.getReadLength() - 1;
if(sr.getMateAlignmentStart() - 1 < recordStart) {
recordStart = sr.getMateAlignmentStart() - 1;
recordStop = sr.getUnclippedEnd();
//Find midpoint if read flag == 3
if(param.getRead() == 3) {
if(sr.getInferredInsertSize()>0) {
FivePrime = sr.getAlignmentStart() - 1 + (sr.getInferredInsertSize() / 2);
} else if(sr.getInferredInsertSize()<0) {
FivePrime = sr.getMateAlignmentStart() - 1 - (sr.getInferredInsertSize() / 2);
} else {
//Most aligners will flag records with an insert size of zero as improper pairs
System.err.println("This statement should never print (insert size=0 when finding midpoint in PileupExtract)");
continue;
}
// Correction to ensure that even insert size mark reoriented for negative strands
if(sr.getInferredInsertSize() % 2 == 0 && read.getDir().equals("-") ) { FivePrime--; }
}

//Find midpoint is read flag == 3
if(param.getRead() == 3) { FivePrime = (recordStart + recordStop) / 2; }

if(recordStop - recordStart < param.getMinInsert() && param.getMinInsert() != -9999) { FivePrime = -1; } //Test for MIN insert size cutoff here
if(recordStop - recordStart > param.getMaxInsert() && param.getMaxInsert() != -9999) { FivePrime = -1; } //Test for MAX insert size cutoff here
} else if(param.getRead() == 3) { FivePrime = -1; } // Make sure that midpoint pileup must come from properly paired read
// Apply insert size filters
if(Math.abs(sr.getInferredInsertSize()) < param.getMinInsert() && param.getMinInsert() != -9999) { continue; } //Test for MIN insert size cutoff here
if(Math.abs(sr.getInferredInsertSize()) > param.getMaxInsert() && param.getMaxInsert() != -9999) { continue; } //Test for MAX insert size cutoff here
} else if(param.getRead() == 3) { continue; } // Make sure that midpoint pileup must come from properly paired read

//Adjust tag start to be within array reference
FivePrime -= (BEDSTART - QUERYWINDOW);
Expand All @@ -119,7 +119,7 @@ else if(param.getTrans() == 2) {
} else if(param.getRead() == 0 || param.getRead() == 2) { //Also outputs if not paired-end since by default it is read-1
int FivePrime = sr.getUnclippedStart() - 1;
if(sr.getReadNegativeStrandFlag()) {
FivePrime = sr.getUnclippedEnd();
FivePrime = sr.getUnclippedEnd() - 1;
FivePrime -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
} else { FivePrime += SHIFT; }
FivePrime -= (BEDSTART - QUERYWINDOW);
Expand Down
11 changes: 4 additions & 7 deletions src/scripts/Read_Analysis/TagPileup.java
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Original file line number Diff line number Diff line change
Expand Up @@ -378,16 +378,13 @@ public Vector<BEDCoord> loadCoord(File INPUT) throws FileNotFoundException {
}
if (Integer.parseInt(temp[1]) >= 0) {
if (temp.length > 4) {
if (temp[5].equals("+")) {
COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]),
"+", name));
if (temp[5].equals("-")) {
COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "-", name));
} else {
COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]),
"-", name));
COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+", name));
}
} else {
COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+",
name));
COORD.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+", name));
}

} else {
Expand Down