Minor fixes

src/bs/bs_aligner.c

@@ -155,7 +155,7 @@ void run_bs_aligner(genome_t *genome2, genome_t *genome1, genome_t *genome,
 
   // Aquí es donde se lanza el workflow, comenzando la creación del fichero alignments.bam
   start_timer(time_start_alig);
-  workflow_run_with(options->num_cpu_threads, wf_input, wf);  
+  workflow_run_with(options->num_cpu_threads, wf_input, wf);
   stop_timer(time_start_alig, time_end_alig, time_alig);
 
   // Log elapsed time

src/bs/methylation.c

@@ -281,18 +281,31 @@ char *obtain_seq(alignment_t *alig, fastq_read_t * orig) {
       if (car == 'D' || car == 'N') {
 	      pos_read += num - 1;
       } else {
-        if (car == 'I' || car == 'H' || car == 'S') {
+        if (car == 'I') {
           for (cont = 0; cont < num; cont++, pos++) {
             if (pos < seq_len) {
               seq[pos] = '-';
             }
           }
         }
+        else{
+        	if (car == 'H' || car == 'S') {
+              	for (cont = 0; cont < num; cont++, pos++, pos_read++) {
+        		if (pos < seq_len) {
+        			seq[pos] = '-';
+        		}
+        	}
+        }
+        }
       }
+
     }
   }
 
-  seq[seq_len - 1] = '\0';
+  //Ricardo, sobreescribe elemento del read, con inserciones se pierde el final del genoma original, con delecciones tamaño más pequeño
+  if (pos < seq_len)
+	  seq[pos] = '\0';
+	  //  seq[seq_len - 1] = '\0';
 
   free(cigar);
   return seq;
@@ -483,7 +496,9 @@ int methylation_status_report(sw_server_input_t* input, batch_t *batch, methylat
   }
 
   // Inicializar listas para guardar datos de c's metiladas/no metiladas
+  //bs_context_t *bs_context = bs_context_new(num_reads, genome->num_chromosomes);
   bs_context_t *bs_context = bs_context_new(10000, genome->num_chromosomes);
+
   mapping_batch->bs_context = bs_context;
 
   remove_duplicates(num_reads, mapping_batch->mapping_lists, mapping_batch->mapping_lists2);
@@ -540,7 +555,15 @@ void add_metilation_status(array_list_t *array_list, bs_context_t *bs_context,
         if (workspace->add_status_seq_dup == NULL) {
           workspace->add_status_seq_dup = strdup(seq);
         } else {
-          strcpy(workspace->add_status_seq_dup, seq);
+        	if (strlen(workspace->add_status_seq_dup)== strlen(seq))
+        	{
+        		strcpy(workspace->add_status_seq_dup, seq);
+        	}
+        	else
+        	{
+        		free(workspace->add_status_seq_dup);
+        		workspace->add_status_seq_dup = strdup(seq);
+        	}
         }
 
         char *seq_dup = workspace->add_status_seq_dup;
@@ -553,6 +576,10 @@ void add_metilation_status(array_list_t *array_list, bs_context_t *bs_context,
       if (workspace->add_status_gen == NULL) {
         workspace->add_status_gen = calloc(len + 6, sizeof(char));
       }
+      else if (strlen(workspace->add_status_gen) != (len + 6)) {
+    	    free(workspace->add_status_gen);
+            workspace->add_status_gen = calloc(len + 6, sizeof(char));
+          }
 
       gen = workspace->add_status_gen;
 

src/hpg-aligner.c

@@ -109,6 +109,8 @@ int main(int argc, char* argv[]) {
   validate_options(options, command);
   LOG_DEBUG_F("Command Mode: %s\n", command);
 
+
+
   if (!strcmp(command, "build-index")) {
     if (options->bs_index == 0) { // Regular index generation
       run_index_builder(options->genome_filename, options->bwt_dirname, options->index_ratio, options->max_num_chromosomes);
@@ -288,6 +290,7 @@ int main(int argc, char* argv[]) {
 
 
 
+
   // BWT index
   LOG_DEBUG("Loading AGT index...");
   bwt_index1 = bwt_index_new(bs_dir1,options->max_num_chromosomes);
@@ -359,6 +362,7 @@ int main(int argc, char* argv[]) {
   }
 
   basic_statistics_display(basic_st, 0, time_alig / 1000000, time_genome / 1000000);
+  basic_statistics_file("basicStatistics.txt",basic_st, 0, time_alig / 1000000, time_genome / 1000000);
   free(basic_st);
   options_free(options);
 

src/statistics.c

@@ -36,6 +36,46 @@ void basic_statistics_display(basic_statistics_t *statistics, int rna_mode, floa
 
 }
 
+
+void basic_statistics_file(char* filename, basic_statistics_t *statistics, int rna_mode, float alig_time, float load_time) {
+
+  FILE *stats_file = fopen(filename,  "w");
+
+
+  size_t total_reads = statistics->total_reads;
+  size_t num_mapped_reads = statistics->num_mapped_reads;
+  size_t total_mappings = statistics->total_mappings;
+
+  size_t total_sp = statistics->total_sp;
+  size_t uniq_sp = statistics->uniq_sp;
+
+  fprintf(stats_file,"+--------------------------------------------------------------------------------------+\n");
+  fprintf(stats_file,"|                                     GLOBAL STATISTICS                                |\n");
+  fprintf(stats_file,"+--------------------------------------------------------------------------------------+\n");
+  fprintf(stats_file,"| Loading Time (s)  : %-65.2f", load_time);
+  fprintf(stats_file,"|\n");
+  fprintf(stats_file,"| Alignment Time (s): %-65.2f", alig_time);
+  fprintf(stats_file,"|\n");
+  fprintf(stats_file,"| Total Time (s)    : %-65.2f", load_time + alig_time);
+  fprintf(stats_file,"|\n");
+  fprintf(stats_file,"========================================================================================\n");
+  fprintf(stats_file,"| Total Reads Processed: %-62llu", total_reads);
+  fprintf(stats_file,"|\n");
+  fprintf(stats_file,"+-------------------------------------------+------------------------------------------+\n");
+  fprintf(stats_file,"| Reads Mapped: %-18llu  %6.2f", num_mapped_reads, num_mapped_reads * 100.0 / total_reads);
+  fprintf(stats_file,"% | ");
+  fprintf(stats_file," Reads Unmapped: %-14llu  %6.2f", total_reads - num_mapped_reads, (total_reads - num_mapped_reads) * 100.0 / total_reads);
+  fprintf(stats_file,"%  |\n");
+  if (rna_mode) {
+    fprintf(stats_file,"+-------------------------------------------+------------------------------------------+\n");
+  } else {
+    fprintf(stats_file,"+-------------------------------------------+------------------------------------------+\n");
+  }
+
+  fclose(stats_file);
+
+}
+
 //------------------------------------------------------------------------------------------
 
 basic_statistics_t *basic_statistics_new() {

src/statistics.h

@@ -39,6 +39,7 @@ extern statistics_t *statistics_p;
 extern basic_statistics_t *basic_st;
 
 void basic_statistics_display(basic_statistics_t *statistics, int rna_mode, float alig_time, float load_time);
+void basic_statistics_file(char* filename, basic_statistics_t *statistics, int rna_mode, float alig_time, float load_time);
 
 void basic_statistics_add(size_t total_reads, size_t num_mapped_reads, size_t total_mappings, basic_statistics_t *basic);