@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

     to work with GMAP and GSNAP from within R. In addition, it provides 

     methods to tally alignment results on a per-nucleotide basis using 

     the bam_tally tool.

-Version: 1.5.4

+Version: 1.5.5

 Depends: R (>= 2.15.0), methods, GenomicRanges

 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),

          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,

@@ -1,4 +1,4 @@

-static char rcsid[] = "$Id: bamtally.c 123356 2014-01-14 00:00:53Z twu $";

+static char rcsid[] = "$Id: bamtally.c 123611 2014-01-15 21:22:04Z twu $";

 #ifdef HAVE_CONFIG_H

 #include <config.h>

 #endif

@@ -701,8 +701,8 @@ Tally_clear (T this) {

   this->n_fromleft_minus = 0;

   if (this->use_array_p == true) {

-#if 0

-    /* print procedures clear each entry */

+#if 1

+    /* Note: these memset instructions are necessary to get correct results */

     memset((void *) this->matches_byshift_plus,0,this->n_matches_byshift_plus * sizeof(int));

     memset((void *) this->matches_byshift_minus,0,this->n_matches_byshift_minus * sizeof(int));

     memset((void *) this->matches_byquality,0,this->n_matches_byquality * sizeof(int));

@@ -2283,6 +2283,7 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

       debug2(printf("data for chrpos %u:\n",chrpos));

       /* Handle insertions at this position */

+      debug2(printf("Pointers for insertions:\n"));

       pointers = push_int(&ignore,pointers,nbytes);

       if (this->insertions_byshift != NULL) {

 	unique_insertions_byshift = NULL;

@@ -2319,6 +2320,7 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

 	qsort(ins_array,ninsertions,sizeof(Insertion_T),Insertion_count_cmp);

 	/* Total number of different insertions at this position */

+	debug2(printf("Number of insertions:\n"));

 	bytes = push_int(&nbytes,bytes,ninsertions);

 	for (i = 0; i < ninsertions; i++) {

 	  ins0 = ins_array[i];

@@ -2355,6 +2357,7 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

       }

       /* Handle deletions at this position */

+      debug2(printf("Pointers for deletions:\n"));

       pointers = push_int(&ignore,pointers,nbytes);

       if (this->deletions_byshift != NULL) {

 	unique_deletions_byshift = NULL;

@@ -2391,6 +2394,7 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

 	qsort(del_array,ndeletions,sizeof(Deletion_T),Deletion_count_cmp);

 	/* Total number of different deletions at this position */

+	debug2(printf("Number of deletions:\n"));

 	bytes = push_int(&nbytes,bytes,ndeletions);

 	for (i = 0; i < ndeletions; i++) {

 	  del0 = del_array[i];

@@ -2428,6 +2432,7 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

       /* Handle allele counts at this position */

+      debug2(printf("Pointers for allele counts:\n"));

       pointers = push_int(&ignore,pointers,nbytes);

       if (pass_variant_filter_p(this->nmatches,this->mismatches_byshift,min_depth,variant_strands) == true) {

 	total_matches_plus = total_matches_minus = 0;

@@ -2461,6 +2466,7 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

 	}

 	/* Total signed counts at this position */

+	debug2(printf("Total signed counts:\n"));

 	bytes = push_int(&nbytes,bytes,total_matches_plus + total_mismatches_plus);

 	bytes = push_int(&nbytes,bytes,total_matches_minus + total_mismatches_minus);

@@ -2884,8 +2890,8 @@ revise_position (char querynt, char genomicnt, int mapq, int quality, int signed

       }

       if (max_shift_plus < this->n_matches_byshift_plus) {

-	/* Clear existing array */

-	memset(this->matches_byshift_plus,0,this->n_matches_byshift_plus * sizeof(int));

+	/* Clear existing array.  Not necessary here if Tally_clear is doing the memset */

+	/* memset(this->matches_byshift_plus,0,this->n_matches_byshift_plus * sizeof(int)); */

       } else {

 	/* Resize array */

 	oldsize = this->n_matches_byshift_plus;

@@ -2899,8 +2905,8 @@ revise_position (char querynt, char genomicnt, int mapq, int quality, int signed

       }

       if (max_shift_minus < this->n_matches_byshift_minus) {

-	/* Clear existing array */

-	memset(this->matches_byshift_minus,0,this->n_matches_byshift_minus * sizeof(int));

+	/* Clear existing array.  Not necessary here if Tally_clear is doing the memset */

+	/* memset(this->matches_byshift_minus,0,this->n_matches_byshift_minus * sizeof(int)); */

       } else {

 	/* Resize array */

 	oldsize = this->n_matches_byshift_minus;