more even assignment to the cores

iprada · Oct 16, 2019 · e7f1bf2 · e7f1bf2
1 parent 6d6ae3b
commit e7f1bf2
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/circlemap/realigner.py b/circlemap/realigner.py
@@ -360,8 +360,7 @@ def realign(self,peaks):
                                         if read.is_read2 == False:
                                             if read.next_reference_start < read.reference_start:
                                                 disorcordants_per_it +=1
-                                                iteration_discordants.append([interval['chrom'], read.next_reference_start,read.reference_start+read.infer_query_length(),
-                                                                              read.qname])
+                                                iteration_discordants.append([interval['chrom'], read.next_reference_start,read.reference_start+read.infer_query_length(),                                                                              read.qname])
 
 
                         #second pass to add discordant read info
@@ -400,6 +399,7 @@ def realign(self,peaks):
             ecc_dna.close()
             genome_fa.close()
 
+
             # Write process output to disk
             output = iteration_merge(only_discordants,results,
                                      self.overlap_fraction,self.split,self.score,

diff --git a/circlemap/utils.py b/circlemap/utils.py
@@ -308,10 +308,15 @@ def bam_circ_sv_peaks(bam,input_bam_name,cores,verbose,pid,clusters):
             while w_start < int(interval[2]):
                 splitted = [interval.chrom, str(w_start), str(w_start + 300)]
                 w_start += 300
-                split_peaks[counter].append(splitted)
+                if counter == chunks:
+                    counter = 0
+                    split_peaks[counter].append(splitted)
+                else:
+                    split_peaks[counter].append(splitted)
+                    counter +=1
         else:
             split_peaks[counter].append([interval.chrom, str(interval.start), str(interval.end)])
-        counter += 1
+            counter += 1
 
 
     return(sorted_bam,split_peaks)