fixes

RevantOrg · Aug 25, 2023 · d3630a9 · d3630a9
1 parent 9551230
commit d3630a9
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Showing 4 changed files with 21 additions and 15 deletions.
diff --git a/scripts/6-repeatAlphabet/1-buildAlphabet.sh b/scripts/6-repeatAlphabet/1-buildAlphabet.sh
@@ -297,10 +297,15 @@ while [ ${ITER} -le ${TANDEM_SPACERS_ITERATIONS} ]; do
 		mv ${READS_TRANSLATED_FILE} ${READS_TRANSLATED_FILE}-preTspacers
 		mv ${READS_TRANSLATED_BOUNDARIES} ${READS_TRANSLATED_BOUNDARIES}-preTspacers
 		mv ${ALPHABET_FILE} ${ALPHABET_FILE}-preTspacers
+        mv ${FULLY_UNIQUE_FILE} ${FULLY_UNIQUE_FILE}-preTspacers
 		for THREAD in $(seq 0 ${TO}); do
 			cat ${TMPFILE_PATH}-tspacers-12-${THREAD}.txt >> ${READS_TRANSLATED_FILE}
 			cat ${TMPFILE_PATH}-tspacers-13-${THREAD}.txt >> ${READS_TRANSLATED_BOUNDARIES}
 		done
+        touch ${FULLY_UNIQUE_FILE}
+        for i in $(sed -n '/^$/=' ${READS_TRANSLATED_FILE}); do
+            echo $(( $i - 1 )) >> ${FULLY_UNIQUE_FILE}
+        done
 		mv ${ALPHABET_FILE_SPACERS} ${ALPHABET_FILE}
 		TANDEM_SPACERS_FIXED="1"
 		echo "Tandem spacers fixed"

diff --git a/src/de/mpi_cbg/revant/apps/BuildAssemblyGraph.java b/src/de/mpi_cbg/revant/apps/BuildAssemblyGraph.java
@@ -217,7 +217,7 @@ public static void main(String[] args) throws IOException {
 		componentSize = new int[nComponents];
 		Math.set(componentSize,nComponents-1,0);
 		for (i=0; i<N_READS; i++) componentSize[component[i]]++;
-        printHistogram(componentSize,nComponents);
+        printHistogram(componentSize,nComponents,N_READS);
 		j=-1;
 		for (i=0; i<nComponents; i++) {
 			if (componentSize[i]>=MIN_COMPONENT_SIZE) componentSize[++j]=i;
@@ -279,7 +279,7 @@ public static void main(String[] args) throws IOException {
 		componentSize = new int[nComponents];
 		Math.set(componentSize,nComponents-1,0);
 		for (i=0; i<N_READS; i++) componentSize[component[i]]++;
-        printHistogram(componentSize,nComponents);
+        printHistogram(componentSize,nComponents,N_READS);
 		j=-1;
 		for (i=0; i<nComponents; i++) {
 			if (componentSize[i]>=MIN_COMPONENT_SIZE) componentSize[++j]=i;
@@ -317,21 +317,21 @@ public static void main(String[] args) throws IOException {
 	}
 
 
-    private static final void printHistogram(int[] componentSize, int nComponents) {
+    private static final void printHistogram(int[] componentSize, int nComponents, int nNodes) {
         int i;
         double count;
         int[] tmpArray;
 
-        System.err.println("Cumulative distribution of component size:");
+        System.err.println("Number of nodes in components of size >=:");
         tmpArray = new int[nComponents];
         System.arraycopy(componentSize,0,tmpArray,0,nComponents);
         Arrays.sort(tmpArray);
-        count=1.0;
-        for (i=1; i<nComponents; i++) {
-            if (tmpArray[i]!=tmpArray[i-1]) System.err.println(tmpArray[i-1]+","+(count/nComponents));
-            count++;
+        count=tmpArray[nComponents-1];
+        for (i=nComponents-2; i>=0; i--) {
+            if (tmpArray[i]!=tmpArray[i+1]) System.err.println(tmpArray[i+1]+","+(count/nNodes));
+            count+=tmpArray[i];
         }
-        System.err.println(tmpArray[nComponents-1]+",1");
+        System.err.println(tmpArray[0]+","+(count/nNodes));
     }
 
 

diff --git a/src/de/mpi_cbg/revant/apps/FixTandemSpacers1.java b/src/de/mpi_cbg/revant/apps/FixTandemSpacers1.java
@@ -54,14 +54,14 @@ public static void main(String[] args) throws IOException {
 
 
 for (int x=0; x<=RepeatAlphabet.lastSpacer; x++) {
-	if (RepeatAlphabet.spacers[x].read==42) System.err.println("VITTU> 1  "+RepeatAlphabet.spacers[x]);
+	if (RepeatAlphabet.spacers[x].read==767) System.err.println("VITTU> 1  "+RepeatAlphabet.spacers[x]);
 }	
 
 		RepeatAlphabet.loadTandemSpacers_blocks(READ_READ_ALIGNMENTS_FILE,DISTANCE_THRESHOLD,LONG_SPACER_LENGTH,NONREPETITIVE_BLOCKS_MODE,tmpArray);
 
 
 for (int x=0; x<=RepeatAlphabet.lastSpacer; x++) {
-	if (RepeatAlphabet.spacers[x].read==42) System.err.println("VITTU> 2  "+RepeatAlphabet.spacers[x]);
+	if (RepeatAlphabet.spacers[x].read==767) System.err.println("VITTU> 2  "+RepeatAlphabet.spacers[x]);
 }	        
 
 
@@ -71,15 +71,15 @@ public static void main(String[] args) throws IOException {
 
 
 for (int x=0; x<=RepeatAlphabet.lastSpacer; x++) {
-	if (RepeatAlphabet.spacers[x].read==42) System.err.println("VITTU> 3  "+RepeatAlphabet.spacers[x]+"  lastSpacerNeighbor="+RepeatAlphabet.lastSpacerNeighbor[x]);
+	if (RepeatAlphabet.spacers[x].read==767) System.err.println("VITTU> 3  "+RepeatAlphabet.spacers[x]+"  lastSpacerNeighbor="+RepeatAlphabet.lastSpacerNeighbor[x]);
 }	        
 
 
 
 		if (!RepeatAlphabet.propagateSolutions(DISTANCE_THRESHOLD_CONSISTENCY)) { System.out.println("3"); return; }
 
 for (int x=0; x<=RepeatAlphabet.lastSpacer; x++) {
-	if (RepeatAlphabet.spacers[x].read==42) System.err.println("VITTU> 4  "+RepeatAlphabet.spacers[x]);
+	if (RepeatAlphabet.spacers[x].read==767) System.err.println("VITTU> 4  "+RepeatAlphabet.spacers[x]);
 }	                
 
 

diff --git a/src/de/mpi_cbg/revant/apps/RepeatAlphabet.java b/src/de/mpi_cbg/revant/apps/RepeatAlphabet.java
@@ -10138,8 +10138,9 @@ public static final void wobble_buildOld2New(Character[] alphabet_old, int lastA
 	 * Remark: wobbling is designed to increase the number of edges in a highly
 	 * disconnected overlap graph where the endpoints of repeat occurrences are uncertain.
 	 * However, such increase in frequency may make some k-mers be classified as repeats 
-	 * rather than as unique addresses on the genome, and this might \emph{remove} some
-	 * edges from the overlap graph.
+	 * rather than as unique addresses in the genome, and this might \emph{remove} some
+	 * edges from the overlap graph (of course it might also make rare noisy k-mers become
+	 * frequent enough to be considered unique addresses in the genome).
 	 *
 	 * Remark: this procedure might put multiple unique characters inside a block that
 	 * contains a single unique character. Thus, throughout the code, no test for the