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fix(qmule and qsv): iSize calculator and qsv throwing exceptions #398

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fix(qmule and qsv): iSize calculator and qsv throwing exceptions #398

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36 changes: 19 additions & 17 deletions q3tiledaligner/src/au/edu/qimr/tiledaligner/util/BLATRecordUtil.java
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -532,29 +532,30 @@ public static List<BLATRecord> removeOverlappingRecords(List<BLATRecord> origina
if (null == originalList) {
throw new IllegalArgumentException("Null list supplied as argument to removeOverlappingRecords!");
}
// if (originalList.size() < 2) return originalList;
int size = originalList.size();
if (size < 2) {
return originalList;
}
List<BLATRecord> nonOverlappingList = new ArrayList<>(size);

List<BLATRecord> nonOverlappingList = new ArrayList<>(size + 1);

/*
* sort the original list
* sort the original list
*/
originalList.sort(null);
/*
* add the entry with the highest score to the new list
*/
nonOverlappingList.add(originalList.get(size - 1));

for (int i = size - 2 ; i >= 0 ; i--) {
if ( ! doesRecordOverlapEntriesInList(nonOverlappingList, originalList.get(i))) {
nonOverlappingList.add(originalList.get(i));
}
}
return nonOverlappingList;

}

/**
Expand Down Expand Up @@ -593,17 +594,18 @@ public static boolean doesRecordOverlapEntriesInList(List<BLATRecord> records, B
* @return
*/
public static boolean doRecordsOverlapReference(BLATRecord r1, BLATRecord r2) {
if (null != r1 && null != r2 && r1.getTName().equals(r2.getTName())) {
int r1Start = r1.getStartPos();
int r1End = r1.getEndPos();
int r2Start = r2.getStartPos();
int r2End = r2.getEndPos();

if ((r2Start >= r1Start && r2Start < r1End) || (r2End > r1Start && r2End <= r1End)) {
return true;
}
}
return false;
if (r1 == null || r2 == null) return false;
final String c1 = r1.getTName();
final String c2 = r2.getTName();
if (c1 == null || !c1.equals(c2)) return false;

final int s1 = r1.getStartPos();
final int e1 = r1.getEndPos();
final int s2 = r2.getStartPos();
final int e2 = r2.getEndPos();

// overlap if max(start) < min(end)
return (s1 < e2) && (s2 < e1);
}

/**
Expand Down
36 changes: 18 additions & 18 deletions q3tiledaligner/src/au/edu/qimr/tiledaligner/util/TARecordUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ public static void trimRangesToRemoveOverlap(int[][] ranges, ChrPosition[] cps)
* trim ranges if there is an overlap
*/
for (int j = 0 ; j < ranges.length - 1; j++) {
if (j + 1 < ranges.length) {
// if (j + 1 < ranges.length) {
int [] thisIntArray = ranges[j];
int [] nextIntArray = ranges[j + 1];
ChrPosition thisCP = cps[j];
Expand Down Expand Up @@ -253,7 +253,7 @@ public static void trimRangesToRemoveOverlap(int[][] ranges, ChrPosition[] cps)

}
}
}
// }
}
}

Expand All @@ -269,16 +269,16 @@ public static void trimRangesToRemoveOverlap(int[][] ranges, ChrPosition[] cps)
* @return
*/
public static int[] sortTileCount(int[] tileCounts) {
return Arrays.stream(tileCounts)
.mapToObj(k -> NumberUtils.splitIntInto2(k))
.sorted((a,b) -> {int diff = Integer.compare((a[0] - a[1]), (b[0] - b[1]));
if (diff == 0) {
diff = b[1] - a[1];
}
return diff;})
.mapToInt(a -> NumberUtils.pack2IntsInto1(a[0], a[1]))
.toArray();

return Arrays.stream(tileCounts)
.mapToObj(NumberUtils::splitIntInto2)
.sorted((a,b) -> {int diff = Integer.compare((a[0] - a[1]), (b[0] - b[1]));
if (diff == 0) {
diff = b[1] - a[1];
}
return diff;})
.mapToInt(a -> NumberUtils.pack2IntsInto1(a[0], a[1]))
.toArray();
}


Expand Down Expand Up @@ -378,7 +378,7 @@ public static TIntObjectMap<Set<IntLongPairs>> getSplitStartPositions(TARecord r
* check that pairs is not a subset of existing pairs
*/
if ( ! IntLongPairsUtil.isPairsASubSetOfExistingPairs(getPairsFromMap(results), pairs)) {
Set<IntLongPairs> resultsListList = results.putIfAbsent(IntLongPairsUtil.getBasesCoveredByIntLongPairs(pairs, seqLength, TILE_LENGTH), new HashSet<>(Arrays.asList(pairs)));
Set<IntLongPairs> resultsListList = results.putIfAbsent(IntLongPairsUtil.getBasesCoveredByIntLongPairs(pairs, seqLength, TILE_LENGTH), new HashSet<>(List.of(pairs)));
if (null != resultsListList) {
resultsListList.add(pairs);
}
Expand Down Expand Up @@ -419,7 +419,7 @@ public static TIntObjectMap<Set<IntLongPairs>> getSplitStartPositions(TARecord r
* check that pairs is not a subset of existing pairs
*/
if ( ! IntLongPairsUtil.isPairsASubSetOfExistingPairs(getPairsFromMap(results), pairs)) {
Set<IntLongPairs> resultsListList = results.putIfAbsent(IntLongPairsUtil.getBasesCoveredByIntLongPairs(pairs, seqLength, TILE_LENGTH), new HashSet<>(Arrays.asList(pairs)));
Set<IntLongPairs> resultsListList = results.putIfAbsent(IntLongPairsUtil.getBasesCoveredByIntLongPairs(pairs, seqLength, TILE_LENGTH), new HashSet<>(List.of(pairs)));
if (null != resultsListList) {
resultsListList.add(pairs);
}
Expand Down Expand Up @@ -455,17 +455,17 @@ public static TIntObjectMap<Set<IntLongPairs>> getSplitStartPositions(TARecord r

public static List<IntLongPairs> getPairsFromMap(TIntObjectMap<Set<IntLongPairs>> map) {
List<IntLongPairs> list = new ArrayList<>();
map.forEachValue(s -> list.addAll(s));
map.forEachValue(list::addAll);
return list;
}

public static IntLongPairs getILPSFromLists(List<IntLongPair> list1, List<IntLongPair> list2, IntLongPair pair) {
List<IntLongPair> results = new ArrayList<>(4);
results.add(pair);
Optional<IntLongPair> list1ILP = getBestILPFromList(list1, pair);
list1ILP.ifPresent(ilp -> results.add(ilp));
list1ILP.ifPresent(results::add);
Optional<IntLongPair> list2ILP = getBestILPFromList(list2, pair);
list2ILP.ifPresent(ilp -> results.add(ilp));
list2ILP.ifPresent(results::add);
results.sort(null);
return new IntLongPairs(results.toArray(new IntLongPair[]{}));
}
Expand Down Expand Up @@ -496,7 +496,7 @@ public static Optional<IntLongPair> getBestILPFromList(List<IntLongPair> list, I
/*
* if leading candidate is too far away from original entry, return empty optional
*/
IntLongPair ilp = list.get(0);
IntLongPair ilp = list.getFirst();
return Optional.of(ilp);

} else {
Expand Down
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