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making changes to reduce size of giant interval lists #1309

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Mar 4, 2019
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making changes to reduce size of giant interval lists #1309

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making changes to reduce size of giant interval lists
lbergelson Feb 22, 2019
8486fc0
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lbergelson Mar 1, 2019
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lbergelson Mar 4, 2019
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8 changes: 7 additions & 1 deletion src/main/java/htsjdk/samtools/util/IntervalList.java
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Original file line number Diff line number Diff line change
Expand Up @@ -531,6 +531,7 @@ public static IntervalList fromReader(final BufferedReader in) {

// Then read in the intervals
final FormatUtil format = new FormatUtil();
String lastSeq = null;
do {
if (line.trim().isEmpty()) {
continue; // skip over blank lines
Expand All @@ -544,7 +545,12 @@ public static IntervalList fromReader(final BufferedReader in) {
}

// Then parse them out
final String seq = fields[SEQUENCE_POS];
String seq = fields[SEQUENCE_POS];
if (seq.equals(lastSeq)) {
seq = lastSeq;
}
lastSeq = seq;

final int start = format.parseInt(fields[START_POS]);
final int end = format.parseInt(fields[END_POS]);
if (start < 1) {
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16 changes: 11 additions & 5 deletions src/main/java/htsjdk/samtools/util/OverlapDetector.java
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Expand Up @@ -82,13 +82,19 @@ public void addLhs(final T object, final Locatable interval) {
final int start = interval.getStart() + this.lhsBuffer;
final int end = interval.getEnd() - this.lhsBuffer;

final Set<T> objects = new HashSet<>(1);
objects.add(object);
final Set<T> newValue = Collections.singleton(object);
if (start <= end) { // Don't put in sequences that have no overlappable bases
final Set<T> alreadyThere = tree.put(start, end, objects);
final Set<T> alreadyThere = tree.put(start, end, newValue);
if (alreadyThere != null) {
alreadyThere.add(object);
tree.put(start, end, alreadyThere);
if( alreadyThere.size() == 1){
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I think that this should be implemented within the IntervalTree class as a computeIfPresent method...

Set<T> mutableSet = new HashSet<>(2);
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hmmm. better find out if you got a mutable one and just add the new element if so...no?

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You mean with an instanceof check? As it's written it should be immutable always if it's exactly size 1 and mutable otherwise. It's a bit awkward but I thought maybe relying on the size was better than relying on the class. I can change that though.

mutableSet.addAll(alreadyThere);
mutableSet.add(object);
tree.put(start, end, mutableSet);
} else {
alreadyThere.add(object);
tree.put(start, end, alreadyThere);
}
}
}
}
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