Parallelized some parts of linear-index building

MANUAL.markdown

@@ -828,8 +828,8 @@ With this mode, you can provide a list of known splice sites, which HISAT2 makes
 You can create such a list using `python extract_splice_sites.py genes.gtf > splicesites.txt`,
 where `extract_splice_sites.py` is included in the HISAT2 package, `genes.gtf` is a gene annotation file,
 and `splicesites.txt` is a list of splice sites with which you provide HISAT2 in this mode.
-Note that it is better to use indexes built using annotated transcripts (such as genome_tran or genome_snp_tran), which works better
-than using this option.  It has no effect to provide splice sites that are already included in indexes.
+Note that it is better to use indexes built using annotated transcripts (such as <i>genome_tran</i> or <i>genome_snp_tran</i>), which works better
+than using this option.  It has no effect to provide splice sites that are already included in the indexes.
 
 </td></tr>
 

aligner_swsse_ee_i16.cpp

@@ -1364,7 +1364,7 @@ bool SwAligner::backtraceNucleotidesEnd2EndSseI16(
 		int readq = (*qu_)[row];
 		assert_leq(col, origCol);
 		// Get score in this cell
-		bool empty, reportedThru, canMoveThru, branch = false;
+		bool empty = false, reportedThru, canMoveThru, branch = false;
 		int cur = SSEMatrix::H;
 		if(!d.mat_.reset_[row]) {
 			d.mat_.resetRow(row);

aligner_swsse_ee_u8.cpp

@@ -1349,7 +1349,7 @@ bool SwAligner::backtraceNucleotidesEnd2EndSseU8(
 		int readq = (*qu_)[row];
 		assert_leq(col, origCol);
 		// Get score in this cell
-		bool empty, reportedThru, canMoveThru, branch = false;
+		bool empty = false, reportedThru, canMoveThru, branch = false;
 		int cur = SSEMatrix::H;
 		if(!d.mat_.reset_[row]) {
 			d.mat_.resetRow(row);

aligner_swsse_loc_i16.cpp

@@ -1721,7 +1721,7 @@ bool SwAligner::backtraceNucleotidesLocalSseI16(
 		int readq = (*qu_)[row];
 		assert_leq(col, origCol);
 		// Get score in this cell
-		bool empty, reportedThru, canMoveThru, branch = false;
+		bool empty = false, reportedThru, canMoveThru, branch = false;
 		int cur = SSEMatrix::H;
 		if(!d.mat_.reset_[row]) {
 			d.mat_.resetRow(row);

aligner_swsse_loc_u8.cpp

@@ -1719,7 +1719,7 @@ bool SwAligner::backtraceNucleotidesLocalSseU8(
 		int readq = (*qu_)[row];
 		assert_leq(col, origCol);
 		// Get score in this cell
-		bool empty, reportedThru, canMoveThru, branch = false;
+		bool empty = false, reportedThru, canMoveThru, branch = false;
 		int cur = SSEMatrix::H;
 		if(!d.mat_.reset_[row]) {
 			d.mat_.resetRow(row);

aln_sink.h

@@ -2402,8 +2402,8 @@ bool AlnSinkWrap<index_t>::report(
 	// Tally overall alignment score
 	TAlScore score = rsa->score().score();
 	if(rsb != NULL) score += rsb->score().score();
-    index_t num_spliced = rsa->num_spliced();
-    if(rsb != NULL) num_spliced += rsb->num_spliced();
+    index_t num_spliced = (index_t)rsa->num_spliced();
+    if(rsb != NULL) num_spliced += (index_t)rsb->num_spliced();
 	// Update best score so far
 	if(paired) {
 		if(score > bestPair_) {