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@fcunial
fcunial committed Aug 3, 2023
1 parent 9738018 commit 541e580
Showing 1 changed file with 43 additions and 8 deletions.
51 changes: 43 additions & 8 deletions src/de/mpi_cbg/revant/apps/RepeatAlphabet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4648,7 +4648,7 @@ public static final void filterAlignments_tandem(String alignmentsFile, boolean
if (!bothReads) {
if ( containedA || identicalA ||
( !filterAlignments_tandem_containsUnique(lastTranslated,startA,endA,nBlocks,lengthA,minIntersection_nonrepetitive) &&
filterAlignments_tandem_allContainedBlueInTandem(readA,lastTranslated,blueIntervalA,startA,endA,nBlocks,lengthA,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD)
filterAlignments_tandem_allContainedBlueInTandem(readA,lastTranslated,blueIntervalA,startA,endA,nBlocks,lengthA,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD,IDENTITY_THRESHOLD)
)
) {
bw.write("0\n"); str=br.readLine(); row++;
Expand All @@ -4658,7 +4658,7 @@ public static final void filterAlignments_tandem(String alignmentsFile, boolean
else {
if ( !identicalA && !containedA &&
( filterAlignments_tandem_containsUnique(lastTranslated,startA,endA,nBlocks,lengthA,minIntersection_nonrepetitive) ||
!filterAlignments_tandem_allContainedBlueInTandem(readA,lastTranslated,blueIntervalA,startA,endA,nBlocks,lengthA,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD)
!filterAlignments_tandem_allContainedBlueInTandem(readA,lastTranslated,blueIntervalA,startA,endA,nBlocks,lengthA,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD,IDENTITY_THRESHOLD)
)
) {
out[1][type]++;
Expand Down Expand Up @@ -4716,7 +4716,7 @@ else if (bothReads) {
if (!bothReads) {
if ( containedB || identicalB ||
( !filterAlignments_tandem_containsUnique(p,startB,endB,nBlocks,lengthB,minIntersection_nonrepetitive) &&
filterAlignments_tandem_allContainedBlueInTandem(readB,p,blueIntervalB,startB,endB,nBlocks,lengthB,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD)
filterAlignments_tandem_allContainedBlueInTandem(readB,p,blueIntervalB,startB,endB,nBlocks,lengthB,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD,IDENTITY_THRESHOLD)
)
) {
bw.write("0\n"); str=br.readLine(); row++;
Expand All @@ -4726,7 +4726,7 @@ else if (bothReads) {
else {
if ( !containedB && !identicalB &&
( filterAlignments_tandem_containsUnique(p,startB,endB,nBlocks,lengthB,minIntersection_nonrepetitive) ||
!filterAlignments_tandem_allContainedBlueInTandem(readB,p,blueIntervalB,startB,endB,nBlocks,lengthB,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD)
!filterAlignments_tandem_allContainedBlueInTandem(readB,p,blueIntervalB,startB,endB,nBlocks,lengthB,TANDEM_DISTANCE_THRESHOLD,DIFFERENCE_THRESHOLD,IDENTITY_THRESHOLD)
)
) {
out[1][type]++;
Expand Down Expand Up @@ -4826,15 +4826,21 @@ private static final int filterAlignments_tandem_isBlue_interval(int blueInterva
* reliable instead, since the boundaries between the units of such a tandem are
* assumed to be clearly defined.
*
* Remark: a blue interval that uses the first or last block of a long-period tandem,
* where the length of such a block is shorter than the length of an interior block,
* is considered reliable instead, since that terminal block might indeed be the
* result of a unique fragmentation process in the genome.
*
* @param distanceThreshold a contained blue interval that coincides with a tandem
* interval, but that is at most this far from the read start/end, is considered
* strictly contained in the tandem interval;
* @param differenceThreshold as defined in $inRedRegion()$.
*/
private static final boolean filterAlignments_tandem_allContainedBlueInTandem(int readID, int boundariesAllID, int blueIntervalsID, int intervalStart, int intervalEnd, int nBlocks, int readLength, int distanceThreshold, int differenceThreshold) {
private static final boolean filterAlignments_tandem_allContainedBlueInTandem(int readID, int boundariesAllID, int blueIntervalsID, int intervalStart, int intervalEnd, int nBlocks, int readLength, int distanceThreshold, int differenceThreshold, int identityThreshold) {
boolean containsBlue, found;
int i, j, k;
int firstBlock, lastBlock, firstPosition, lastPosition, lastBlueInterval, lastTandemInterval;
int from, to, block, firstLength, lastLength, middleLength;

if (blueIntervalsID==-1) return false;
lastBlueInterval=blueIntervals[blueIntervalsID].length-1;
Expand All @@ -4847,7 +4853,7 @@ private static final boolean filterAlignments_tandem_allContainedBlueInTandem(in
else firstPosition=boundaries_all[boundariesAllID][firstBlock-1];
if (firstPosition>=intervalEnd) break;
lastBlock=firstBlock+blueIntervals[blueIntervalsID][i+1]-1;
if (lastBlock==nBlocks-1) lastPosition=Reads.getReadLength(readID)-1;
if (lastBlock==nBlocks-1) lastPosition=readLength-1;
else lastPosition=boundaries_all[boundariesAllID][lastBlock];
if (lastPosition<=intervalStart) continue;
if ( Intervals.isApproximatelyContained(firstPosition,lastPosition,intervalStart,intervalEnd) &&
Expand All @@ -4861,8 +4867,37 @@ private static final boolean filterAlignments_tandem_allContainedBlueInTandem(in
continue;
}
if (tandems[readID][j]>firstBlock) break;
if ( tandems[readID][j]<firstBlock || tandems[readID][j+1]>lastBlock ||
(tandems[readID][j]==firstBlock && tandems[readID][j+1]==lastBlock && (isBlockPeriodic(boundariesAllID,firstBlock) || firstPosition<distanceThreshold || lastPosition>readLength-distanceThreshold))
block=tandems[readID][j];
from=block==0?0:boundaries_all[boundariesAllID][block-1];
to=block==nBlocks-1?readLength-1:boundaries_all[boundariesAllID][block];
firstLength=to-from+1;
if (tandems[readID][j+1]!=tandems[readID][j]) {
block=tandems[readID][j+1];
from=block==0?0:boundaries_all[boundariesAllID][block-1];
to=block==nBlocks-1?readLength-1:boundaries_all[boundariesAllID][block];
lastLength=to-from+1;
if (tandems[readID][j+1]==tandems[readID][j]+1) middleLength=0;
else {
block=tandems[readID][j]+1;
from=block==0?0:boundaries_all[boundariesAllID][block-1];
block=tandems[readID][j+1]-1;
to=block==nBlocks-1?readLength-1:boundaries_all[boundariesAllID][block];
middleLength=(to-from+1)/(tandems[readID][j+1]-tandems[readID][j]-1);
}
}
else { lastLength=firstLength; middleLength=0; }
if ( ( isBlockPeriodic(boundariesAllID,tandems[readID][j]) &&
( tandems[readID][j]<firstBlock || tandems[readID][j+1]>lastBlock ||
(tandems[readID][j]==firstBlock && tandems[readID][j+1]==lastBlock && (firstPosition<distanceThreshold || lastPosition>readLength-distanceThreshold))
)
) ||
( !isBlockPeriodic(boundariesAllID,tandems[readID][j]) &&
( (tandems[readID][j]==firstBlock && tandems[readID][j+1]>lastBlock && firstLength>=middleLength-identityThreshold) ||
(tandems[readID][j+1]==lastBlock && tandems[readID][j]<firstBlock && lastLength>=middleLength-identityThreshold) ||
(tandems[readID][j]<firstBlock && tandems[readID][j+1]>lastBlock) ||
(tandems[readID][j]==firstBlock && tandems[readID][j+1]==lastBlock && (firstPosition<distanceThreshold || lastPosition>readLength-distanceThreshold))
)
)
) {
found=true;
break;
Expand Down

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