Small improvements to reorder algorithm

hit.h

@@ -253,9 +253,8 @@ class HitSink {
 			}
 		}
 		ptCounts_[threadId]++;
-		size_t batchId = (size_t)(p.rdid()/perThreadBufSize_);
 		if (reorder_ && reorderInfo_[threadId].flushed) {
-			reorderInfo_[threadId].batchId = batchId;
+			reorderInfo_[threadId].batchId = p.batch_id();
 			reorderInfo_[threadId].flushed = false;
 		}
 		maybeFlush(threadId);

pat.h

@@ -962,7 +962,8 @@ class PatternSourcePerThread {
 		last_batch_(false),
 		last_batch_size_(0),
 		skip_(skip),
-		seed_(seed) { }
+		seed_(seed),
+		batch_id_(0) { }
 
 	/**
 	 * Get the next paired or unpaired read from the wrapped
@@ -980,6 +981,8 @@ class PatternSourcePerThread {
 
 	TReadId rdid() const { return buf_.rdid(); }
 
+	size_t batch_id() const { return batch_id_; }
+
 	/**
 	 * Return true iff the read currently in the buffer is a
 	 * paired-end read.
@@ -1002,6 +1005,7 @@ class PatternSourcePerThread {
 		buf_.reset();
 		std::pair<bool, int> res = composer_.nextBatch(buf_);
 		buf_.init();
+		batch_id_ = (size_t)(buf_.rdid()/buf_.max_buf_);
 		return res;
 	}
 
@@ -1033,6 +1037,7 @@ class PatternSourcePerThread {
 	size_t last_batch_size_;  // # reads read in previous batch
 	uint32_t skip_;           // skip reads with rdids less than this
 	uint32_t seed_;           // pseudo-random seed based on read content
+	size_t batch_id_;	  // identify batches of reads for reordering
 };
 
 /**

sam.cpp

@@ -116,9 +116,8 @@ void SAMHitSink::reportUnOrMax(
 		o << '\n';
 	}
 	ptCounts_[threadId]++;
-	size_t batchId = (size_t)(p.rdid()/perThreadBufSize_);
 	if (reorder_ && reorderInfo_[threadId].flushed) {
-		reorderInfo_[threadId].batchId = batchId;
+		reorderInfo_[threadId].batchId = p.batch_id();
 		reorderInfo_[threadId].flushed = false;
 	}
 	maybeFlush(threadId);