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owlangowlang
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rename variables in PileupExtract
Two variables renamed in PileupExtract: BEDCoord `read` renamed to `coord` and int variable specifying marked location of for pileup renamed from `FivePrime` to `mark` The BEDCoord is renamed to specify it as different from the SAMRecord objects. The int type variable is renamed `mark` because the variable is/will be used to mark features other than just the FivePrime end including the three prime end and midpoint.
1 parent c65f746 commit d312227

1 file changed

Lines changed: 32 additions & 32 deletions

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‎src/scripts/Read_Analysis/PileupScripts/PileupExtract.java‎

Lines changed: 32 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ public PileupExtract(PileupParameters p, File b, Vector<BEDCoord> i, int current
3535
subsetsize = length;
3636
}
3737

38-
public void extract(BEDCoord read) {
38+
public void extract(BEDCoord coord) {
3939
double[] TAG_S1 = null;
4040
double[] TAG_S2 = null;
4141
int SHIFT = param.getShift();
@@ -46,8 +46,8 @@ public void extract(BEDCoord read) {
4646
int MIDPOINT_ADJUST = 0;
4747
if(param.getRead() == 3) { MIDPOINT_ADJUST = 300; }
4848

49-
int BEDSTART = (int)read.getStart();
50-
int BEDSTOP = (int)read.getStop();
49+
int BEDSTART = (int)coord.getStart();
50+
int BEDSTOP = (int)coord.getStop();
5151

5252
//Correct Window Size for proper transformations
5353
int WINDOW = (BEDSTOP - BEDSTART) + ((param.getBin() / 2) * 2);
@@ -64,7 +64,7 @@ else if(param.getTrans() == 2) {
6464
if(STRAND == 0) TAG_S2 = new double[WINDOW];
6565

6666
//SAMRecords are 1-based
67-
CloseableIterator<SAMRecord> iter = inputSam.query(read.getChrom(), BEDSTART - QUERYWINDOW - SHIFT - MIDPOINT_ADJUST - 1, BEDSTOP + QUERYWINDOW + SHIFT + MIDPOINT_ADJUST + 1, false);
67+
CloseableIterator<SAMRecord> iter = inputSam.query(coord.getChrom(), BEDSTART - QUERYWINDOW - SHIFT - MIDPOINT_ADJUST - 1, BEDSTOP + QUERYWINDOW + SHIFT + MIDPOINT_ADJUST + 1, false);
6868
while (iter.hasNext()) {
6969
//Create the record object
7070
//SAMRecord is 1-based
@@ -74,72 +74,72 @@ else if(param.getTrans() == 2) {
7474
if((sr.getProperPairFlag() && param.getPErequire()) || !param.getPErequire()) { //Must either be properly paired if paired-end or don't care about requirement
7575
//Read 1 and want Read 1, Read 2 and want Read 2, want any read, Read 1 and want midpoint
7676
if((sr.getFirstOfPairFlag() && param.getRead() == 0) || (!sr.getFirstOfPairFlag() && param.getRead() == 1) || param.getRead() == 2 || (sr.getFirstOfPairFlag() && param.getRead() == 3)) {
77-
int FivePrime = sr.getUnclippedStart() - 1;
77+
int mark = sr.getUnclippedStart() - 1;
7878
if(sr.getReadNegativeStrandFlag()) {
79-
FivePrime = sr.getUnclippedEnd() - 1;
80-
FivePrime -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
81-
} else { FivePrime += SHIFT; }
79+
mark = sr.getUnclippedEnd() - 1;
80+
mark -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
81+
} else { mark += SHIFT; }
8282

8383
if(sr.getProperPairFlag()) { //prevent cases where non-properly paired Read1 gets to this point
8484
//Find midpoint if read flag == 3
8585
if(param.getRead() == 3) {
8686
if(sr.getInferredInsertSize()>0) {
87-
FivePrime = sr.getAlignmentStart() - 1 + (sr.getInferredInsertSize() / 2);
87+
mark = sr.getAlignmentStart() - 1 + (sr.getInferredInsertSize() / 2);
8888
} else if(sr.getInferredInsertSize()<0) {
89-
FivePrime = sr.getMateAlignmentStart() - 1 - (sr.getInferredInsertSize() / 2);
89+
mark = sr.getMateAlignmentStart() - 1 - (sr.getInferredInsertSize() / 2);
9090
} else {
9191
//Most aligners will flag records with an insert size of zero as improper pairs
9292
System.err.println("This statement should never print (insert size=0 when finding midpoint in PileupExtract)");
9393
continue;
9494
}
9595
// Correction to ensure that even insert size mark reoriented for negative strands
96-
if(sr.getInferredInsertSize() % 2 == 0 && read.getDir().equals("-") ) { FivePrime--; }
96+
if(sr.getInferredInsertSize() % 2 == 0 && coord.getDir().equals("-") ) { mark--; }
9797
}
9898
// Apply insert size filters
9999
if(Math.abs(sr.getInferredInsertSize()) < param.getMinInsert() && param.getMinInsert() != -9999) { continue; } //Test for MIN insert size cutoff here
100100
if(Math.abs(sr.getInferredInsertSize()) > param.getMaxInsert() && param.getMaxInsert() != -9999) { continue; } //Test for MAX insert size cutoff here
101101
} else if(param.getRead() == 3) { continue; } // Make sure that midpoint pileup must come from properly paired read
102102

103103
//Adjust tag start to be within array reference
104-
FivePrime -= (BEDSTART - QUERYWINDOW);
104+
mark -= (BEDSTART - QUERYWINDOW);
105105

106106
//Increment Final Array keeping track of pileup
107-
if(FivePrime >= 0 && FivePrime < TAG_S1.length) {
107+
if(mark >= 0 && mark < TAG_S1.length) {
108108
if(STRAND == 0) {
109-
if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S2[FivePrime] += 1; }
110-
else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S2[FivePrime] += 1; }
111-
else if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S1[FivePrime] += 1; }
112-
else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S1[FivePrime] += 1;}
109+
if(!sr.getReadNegativeStrandFlag() && coord.getDir().equals("-")) { TAG_S2[mark] += 1; }
110+
else if(sr.getReadNegativeStrandFlag() && coord.getDir().equals("+")) { TAG_S2[mark] += 1; }
111+
else if(!sr.getReadNegativeStrandFlag() && coord.getDir().equals("+")) { TAG_S1[mark] += 1; }
112+
else if(sr.getReadNegativeStrandFlag() && coord.getDir().equals("-")) { TAG_S1[mark] += 1;}
113113
} else {
114-
TAG_S1[FivePrime] += 1;
114+
TAG_S1[mark] += 1;
115115
}
116116
}
117117
}
118118
}
119119
} else if(param.getRead() == 0 || param.getRead() == 2) { //Also outputs if not paired-end since by default it is read-1
120-
int FivePrime = sr.getUnclippedStart() - 1;
120+
int mark = sr.getUnclippedStart() - 1;
121121
if(sr.getReadNegativeStrandFlag()) {
122-
FivePrime = sr.getUnclippedEnd() - 1;
123-
FivePrime -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
124-
} else { FivePrime += SHIFT; }
125-
FivePrime -= (BEDSTART - QUERYWINDOW);
122+
mark = sr.getUnclippedEnd() - 1;
123+
mark -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
124+
} else { mark += SHIFT; }
125+
mark -= (BEDSTART - QUERYWINDOW);
126126

127127
//Increment Final Array keeping track of pileup
128-
if(FivePrime >= 0 && FivePrime < TAG_S1.length) {
128+
if(mark >= 0 && mark < TAG_S1.length) {
129129
if(STRAND == 0) {
130-
if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S2[FivePrime] += 1; }
131-
else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S2[FivePrime] += 1; }
132-
else if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S1[FivePrime] += 1; }
133-
else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S1[FivePrime] += 1;}
130+
if(!sr.getReadNegativeStrandFlag() && coord.getDir().equals("-")) { TAG_S2[mark] += 1; }
131+
else if(sr.getReadNegativeStrandFlag() && coord.getDir().equals("+")) { TAG_S2[mark] += 1; }
132+
else if(!sr.getReadNegativeStrandFlag() && coord.getDir().equals("+")) { TAG_S1[mark] += 1; }
133+
else if(sr.getReadNegativeStrandFlag() && coord.getDir().equals("-")) { TAG_S1[mark] += 1;}
134134
} else {
135-
TAG_S1[FivePrime] += 1;
135+
TAG_S1[mark] += 1;
136136
}
137137
}
138138
}
139139
}
140140
iter.close();
141141

142-
if(read.getDir().equals("-")) {
142+
if(coord.getDir().equals("-")) {
143143
TAG_S1 = ArrayUtilities.reverseArray(TAG_S1);
144144
TAG_S2 = ArrayUtilities.reverseArray(TAG_S2);
145145
}
@@ -176,7 +176,7 @@ else if(param.getTrans() == 2) {
176176
}
177177
}
178178

179-
read.setFstrand(finalF);
180-
read.setRstrand(finalR);
179+
coord.setFstrand(finalF);
180+
coord.setRstrand(finalR);
181181
}
182182
}

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