Verify that the suffix array sample interval is a power of 2

src/BuildSalmonIndex.cpp

@@ -137,6 +137,12 @@ bool buildAuxKmerIndex(boost::filesystem::path& outputPrefix, uin32_t k,
 }
 */
 
+// Cool way to do this from 
+// http://stackoverflow.com/questions/108318/whats-the-simplest-way-to-test-whether-a-number-is-a-power-of-2-in-c
+bool isPowerOfTwo(uint32_t n) {
+  return (n > 0 and (n & (n-1)) == 0);
+}
+
 int salmonIndex(int argc, char* argv[]) {
 
     using std::string;
@@ -160,7 +166,8 @@ int salmonIndex(int argc, char* argv[]) {
     ("sasamp,s", po::value<uint32_t>(&saSampInterval)->default_value(1)->required(),
                             "The interval at which the suffix array should be sampled. "
                             "Smaller values are faster, but produce a larger index. "
-                            "The default should be OK, unless your transcriptome is huge.")
+                            "The default should be OK, unless your transcriptome is huge. "
+			    "This value should be a power of 2.")
     ;
 
     po::variables_map vm;
@@ -181,6 +188,14 @@ Creates a salmon index.
         }
         po::notify(vm);
 
+	uint32_t sasamp = vm["sasamp"].as<uint32_t>();
+	if (!isPowerOfTwo(sasamp)) {
+	  fmt::MemoryWriter errWriter;
+	  errWriter << "Error: The suffix array sampling interval must be "
+		       "a power of 2. The value provided, " << sasamp << ", is not.";
+	  throw(std::logic_error(errWriter.str()));
+	}
+
         fmt::MemoryWriter optWriter;
         optWriter << vm["sasamp"].as<uint32_t>();
 

src/FragmentStartPositionDistribution.cpp

@@ -98,14 +98,19 @@ double FragmentStartPositionDistribution::operator()(
         int32_t hitPos,
         uint32_t txpLen,
         double logEffLen) {
+
+    if (hitPos < 0) { hitPos = 0; }
     assert(hitPos < txpLen);
+    if (hitPos >= txpLen) {
+	    std::cerr << "\n\nhitPos = " << hitPos << ", txpLen = " << txpLen << "!!\n\n\n";
+	    return salmon::math::LOG_0;
+    }
     // If we haven't updated the CDF yet, then
     // just return log(1 / effLen);
     if (!isUpdated_) {
         return -logEffLen;
     }
 
-    if (hitPos < 0) { hitPos = 0; }
     double a = hitPos * (1.0 / txpLen);
 
     double effLen = std::exp(logEffLen);

src/SalmonQuantify.cpp

@@ -1250,7 +1250,7 @@ template <typename CoverageCalculator>
 inline bool nearEndOfTranscript(
             CoverageCalculator& hit,
             Transcript& txp,
-            uint32_t cutoff=200) {
+            int32_t cutoff=std::numeric_limits<int32_t>::max()) {
 	// check if hit appears close to the end of the given transcript
 	auto hitPos = hit.bestHitPos;
 	return (hitPos < cutoff or std::abs(txp.RefLength - hitPos) < cutoff);
@@ -1380,7 +1380,7 @@ void getHitsForFragment(std::pair<header_sequence_qual, header_sequence_qual>& f
     uint32_t firstTranscriptID = std::numeric_limits<uint32_t>::max();
     double bestScore = -std::numeric_limits<double>::max();
     if (BOOST_UNLIKELY(isOrphan)) {
-        return;
+        //return;
         bool foundValidHit{false};
         // search for a hit on the left
         for (auto& tHitList : leftHits) {