*** empty log message ***

ebwt_search.cpp

@@ -136,6 +136,7 @@ static const char * refMapFile  = NULL;  // file containing a map from index coo
 static const char * annotMapFile= NULL;  // file containing a map from reference coordinates to annotations
 static size_t fastaContLen      = 0;
 static size_t fastaContFreq     = 0;
+static bool hadoopOut           = false; // print Hadoop status and summary messages
 
 // mating constraints
 
@@ -212,7 +213,8 @@ enum {
 	ARG_CHAININ,
 	ARG_REFMAP,
 	ARG_ANNOTMAP,
-	ARG_REPORTSE
+	ARG_REPORTSE,
+	ARG_HADOOPOUT
 };
 
 static struct option long_options[] = {
@@ -316,6 +318,7 @@ static struct option long_options[] = {
 	{(char*)"refmap",       required_argument, 0,            ARG_REFMAP},
 	{(char*)"annotmap",     required_argument, 0,            ARG_ANNOTMAP},
 	{(char*)"reportse",     no_argument,       0,            ARG_REPORTSE},
+	{(char*)"hadoopout",    no_argument,       0,            ARG_HADOOPOUT},
 	{(char*)0, 0, 0, 0} // terminator
 };
 
@@ -1448,6 +1451,7 @@ static void parseOptions(int argc, char **argv) {
 #endif
 	   		}
 	   		case ARG_MMSWEEP: mmSweep = true; break;
+	   		case ARG_HADOOPOUT: hadoopOut = true; break;
 	   		case ARG_DUMP_NOHIT: dumpNoHits = new ofstream(".nohits.dump"); break;
 	   		case ARG_DUMP_HHHIT: dumpHHHits = new ofstream(".hhhits.dump"); break;
 	   		case ARG_AL: dumpAlBase = optarg; break;
@@ -4484,7 +4488,7 @@ static void driver(const char * type,
 			delete ebwtBw;
 		}
 		if(!quiet) {
-			sink->finish(); // end the hits section of the hit file
+			sink->finish(hadoopOut); // end the hits section of the hit file
 		}
 		if(dumpHHHits != NULL) dumpHHHits->close();
 		if(dumpNoHits != NULL) dumpNoHits->close();

hit.h

@@ -588,7 +588,7 @@ class HitSink {
 	 * Called when all alignments are complete.  It is assumed that no
 	 * synchronization is necessary.
 	 */
-	void finish() {
+	void finish(bool hadoopOut) {
 		// Close output streams
 		closeOuts();
 		if(!quiet_) {
@@ -634,6 +634,13 @@ class HitSink {
 					 << " singleton alignments to " << _outs.size()
 					 << " output stream(s)" << endl;
 			}
+			if(hadoopOut) {
+				cerr << "reporter:counter:Bowtie,reads_with_at_least_1_alignment," << numAligned_ << endl;
+				cerr << "reporter:counter:Bowtie,reads_with_no_alignments," << numUnaligned_ << endl;
+				cerr << "reporter:counter:Bowtie,reads_over_dash_m_limit," << numMaxed_ << endl;
+				cerr << "reporter:counter:Bowtie,unpaired_alignments_reported," << numReported_ << endl;
+				cerr << "reporter:counter:Bowtie,paired_alignments_reported," << numReportedPaired_ << endl;
+			}
 		}
 		// Print the recalibration table.
 		if(recalTable_ != NULL) {

shmem.cpp

@@ -16,6 +16,9 @@
 
 using namespace std;
 
+#define SHMEM_UNINIT  0xafba4242
+#define SHMEM_INIT    0xffaa6161
+
 /**
  * Tries to allocate a shared-memory chunk for a given file of a given size.
  */
@@ -95,14 +98,15 @@ bool allocSharedMem(string fname,
 		}
 	} // while(true)
 	*dst = ptr;
-	if(ds.shm_cpid == getpid()) {
+	bool initid = (((volatile uint32_t*)((char*)ptr + len))[0] == SHMEM_INIT);
+	if(ds.shm_cpid == getpid() && !initid) {
 		if(verbose) {
 			cerr << "  I (pid = " << getpid() << ") created the "
 			     << "shared memory for " << memName << endl;
 		}
 		// Set this value just off the end of the chunk to
 		// indicate that the data hasn't been read yet.
-		((volatile uint32_t*)((char*)ptr + len))[0] = 0xffffffff;
+		((volatile uint32_t*)((char*)ptr + len))[0] = SHMEM_UNINIT;
 		return true;
 	} else {
 		if(verbose) {
@@ -119,16 +123,16 @@ bool allocSharedMem(string fname,
  * finished initializing it.
  */
 void notifySharedMem(void *mem, size_t len) {
-	((volatile uint32_t*)((char*)mem + len))[0] = 0x0f0f0f0f;
+	((volatile uint32_t*)((char*)mem + len))[0] = SHMEM_INIT;
 }
 
 /**
  * Wait until the leader of a shared-memory chunk has finished
  * initializing it.
  */
 void waitSharedMem(void *mem, size_t len) {
-	while(((volatile uint32_t*)((char*)mem + len))[0] != 0x0f0f0f0f) {
-		// spin
+	while(((volatile uint32_t*)((char*)mem + len))[0] != SHMEM_INIT) {
+		sleep(1);
 	}
 }
 

str_util.h

@@ -13,7 +13,14 @@ hash_string(const std::string& s) {
 	int b = 378551;
 	for(size_t i = 0; i < s.length(); i++) {
 		ret = (ret * a) + (int)s[i];
-		a *= b;
+		if(a == 0) {
+			a += b;
+		} else {
+			a *= b;
+		}
+		if(a == 0) {
+			a += b;
+		}
 	}
 	return ret;
 }