MErge conflicts

CHANGES.md

@@ -4,6 +4,10 @@
 
 * Making species and assembly required commandline arguments in the estep
 
+## 1.13.15
+
+* Add checks to sam_iter_next to ensure result is checked for errors
+
 ## 1.13.14
 
 * Fix array length index, check loop length and error messages related to 1.13.13.

Makefile

@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.14
+CAVEMAN_VERSION=1.13.15
 
 TEST_REF?=""
 #Compiler

src/bam_access.c

@@ -408,9 +408,7 @@ file_holder *bam_access_get_by_position_counts_stranded(char *norm_file, char *c
       check(res==0,"Error running pileup callback");
     }//End of while we have pileup reads
   }
-  if(result != -1){
-    fprintf(stderr,"SAMTOOLS ERROR %d\n",result);
-  }
+  check(result >= -1, "Error detected (%d) when trying to iterate through region.",result);
 	bam_plp_push(buf,0); // finalize pileup
   sam_itr_destroy(iter);
   //Now for the pileup method
@@ -1243,7 +1241,7 @@ List *bam_access_get_sorted_reads_at_this_pos(char *chr_name, uint32_t start, ui
     }
 
   }//End of while iterator to populate pileup
-
+  check(result >= -1, "Error detected (%d) when trying to iterate through region.",result);
   sam_itr_destroy(iter);
 	bam_plp_push(buf,0); // finalize pileup
 
@@ -1336,10 +1334,17 @@ int bam_access_get_count_with_bam(char *chr_name, uint32_t start, uint32_t stop,
     counter++;
 
   }//End of iteration through reads in this region
+  check(result >= -1, "Error detected (%d) when trying to iterate through region.",result);
   sam_itr_destroy(iter);
   bam_destroy1(b);
   free(region);
   return counter;
+
+error:
+  if(iter) sam_itr_destroy(iter);
+  if(b) bam_destroy1(b);
+  if(region) free(region);
+  return -1;
 }
 
 void bam_access_include_sw(int inc){

src/split.c

@@ -278,6 +278,7 @@ int split_main(int argc, char *argv[]){
 
 			while(curr_n_pos<=curr_t_pos && iter_n_status>=0 && iter_t_status>=0 && rd_count<=max_read_count){ //While the positions aren't equal and tumour has reads left. Normal jumps ahead
 				iter_n_status = sam_itr_next(sf_norm,iter_norm,norm_read);
+        check(iter_n_status>=-1,"Error detected (%d) when trying to iterate through region.",iter_n_status);
 				curr_n_pos = norm_read->core.pos;
 				if(iter_n_status>=0 && bam_access_check_bam_flags(norm_read) == 1 && ignore_reg_access_get_ign_reg_overlap(curr_n_pos,ignore_regs,ignore_reg_count) == NULL){
 					rd_count++;
@@ -286,6 +287,7 @@ int split_main(int argc, char *argv[]){
 
 			while(curr_t_pos<=curr_n_pos && iter_t_status>=0 && iter_n_status>=0){ //While the positions aren't equal and normal has reads left
 				iter_t_status = sam_itr_next(sf_tum,iter_tum,tum_read);
+        check(iter_t_status>=-1,"Error detected (%d) when trying to iterate through region.",iter_t_status);
 				curr_t_pos = tum_read->core.pos;
 				if(iter_t_status>=0 && bam_access_check_bam_flags(tum_read) == 1 && ignore_reg_access_get_ign_reg_overlap(curr_t_pos,ignore_regs,ignore_reg_count) == NULL){
 					rd_count++;
@@ -296,6 +298,7 @@ int split_main(int argc, char *argv[]){
 			if(iter_n_status<0 && iter_t_status>=0){ //No more normal reads
 				while(iter_t_status>=0 && rd_count<=max_read_count){
 					iter_t_status = sam_itr_next(sf_tum,iter_tum,tum_read);
+          check(iter_t_status>=-1,"Error detected (%d) when trying to iterate through region.",iter_t_status);
 					curr_t_pos = tum_read->core.pos;
 					if(iter_t_status>=0 && bam_access_check_bam_flags(tum_read) == 1 && ignore_reg_access_get_ign_reg_overlap(curr_t_pos,ignore_regs,ignore_reg_count) == NULL){
 				 		rd_count++;
@@ -306,6 +309,7 @@ int split_main(int argc, char *argv[]){
 			if(iter_t_status<0 && iter_n_status>=0){ //No more tumour reads
 				while(iter_n_status>=0 && rd_count<=max_read_count){
 					iter_n_status = sam_itr_next(sf_norm,iter_norm,norm_read);
+          check(iter_n_status>=-1,"Error detected (%d) when trying to iterate through region.",iter_n_status);
 					curr_n_pos = norm_read->core.pos;
 					if(iter_n_status>=0 && bam_access_check_bam_flags(norm_read) == 1 && ignore_reg_access_get_ign_reg_overlap(curr_n_pos,ignore_regs,ignore_reg_count) == NULL){
 						rd_count++;