Upping to v0.97

demo/demo.bash

@@ -5,7 +5,7 @@
 # Path to ABRA jar file (with dependencies)
 # If you've downloaded the jar, set this to the appropriate location
 # Compiled jars will be under the target directory
-JAR=../target/abra-0.96-SNAPSHOT-jar-with-dependencies.jar
+JAR=../target/abra-0.97-SNAPSHOT-jar-with-dependencies.jar
 
 # Path to hg19 reference (indexed by BWA)
 #REF=/datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/ref/GRCh37-lite.fa

pom.xml

@@ -5,7 +5,7 @@
 
   <groupId>abra</groupId>
   <artifactId>abra</artifactId>
-  <version>0.96-SNAPSHOT</version>
+  <version>0.97-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <name>abra</name>

src/main/c/assembler.c

@@ -20,7 +20,7 @@ using google::sparse_hash_set;
 //#define MIN_CONTIG_LENGTH 101
 //#define MIN_NODE_FREQUENCY 3
 //#define MIN_NODE_FREQUENCY 2
-#define MAX_CONTIG_SIZE 5000
+#define MAX_CONTIG_SIZE 50000
 #define MAX_READ_LENGTH 1001
 //#define MIN_BASE_QUALITY 20
 #define INCREASE_MIN_NODE_FREQ_THRESHOLD 1600
@@ -652,12 +652,14 @@ void prune_graph(sparse_hash_map<const char*, struct node*, my_hash, eqstr>* nod
 	int freq = min_node_freq;
 
 	if (!isUnalignedRegion) {
+		/*
 		int increase_freq = nodes->size() / INCREASE_MIN_NODE_FREQ_THRESHOLD;
 
 		if (increase_freq > 0) {
 			freq = freq + increase_freq;
 //			printf("Increased mnf to: %d for nodes size: %d\n", freq, nodes->size());
 		}
+		*/
 	}
 
 	if (freq > 1) {
@@ -1151,7 +1153,7 @@ extern "C"
 	max_nodes = j_max_nodes;
 
 	if (debug) {
-		printf("Abra JNI entry point v0.96, prefix: %s, read_length: %d, kmer_size: %d, min_node_freq: %d, min_base_qual: %d, min_edge_ratio %f, debug: %d, max_nodes: %d\n",
+		printf("Abra JNI entry point v0.97, prefix: %s, read_length: %d, kmer_size: %d, min_node_freq: %d, min_base_qual: %d, min_edge_ratio %f, debug: %d, max_nodes: %d\n",
 				prefix, read_length, kmer_size, min_node_freq, min_base_quality, min_edge_ratio, debug, max_nodes);
 	}
 

src/main/java/abra/ReAligner.java

@@ -700,10 +700,10 @@ private boolean isAnyElementDifferent(List<String> elems) {
 	static List<Feature> getRegions(String regionsBed, int readLength, boolean hasPresetKmers) throws IOException {
 		RegionLoader loader = new RegionLoader();
 		List<Feature> regions = loader.load(regionsBed, hasPresetKmers);
-		if (regions.size() > 0 && (regions.get(0).getKmer() == 0)) {
-			regions = RegionLoader.collapseRegions(regions, readLength);
-			regions = splitRegions(regions);
-		}
+//		if (regions.size() > 0 && (regions.get(0).getKmer() == 0)) {
+//			regions = RegionLoader.collapseRegions(regions, readLength);
+//			regions = splitRegions(regions);
+//		}
 
 		return regions;
 	}
@@ -1055,7 +1055,7 @@ private NativeAssembler newAssembler(Feature region) {
 		assem.setMaxContigs(assemblerSettings
 				.getMaxPotentialContigs());
 
-		assem.setMaxPathsFromRoot(100000);
+		assem.setMaxPathsFromRoot(100000000);
 		assem.setReadLength(readLength);
 		//assem.setKmer(assemblerSettings.getKmerSize());
 		assem.setKmer(getKmers(region));
@@ -1191,7 +1191,7 @@ boolean isFiltered(SAMRecord read) {
 
 	public static void run(String[] args) throws Exception {
 
-		System.out.println("Starting 0.96 ...");
+		System.out.println("Starting 0.97 ...");
 
 		ReAlignerOptions options = new ReAlignerOptions();
 		options.parseOptions(args);