fix quantify mode output order

Author: cheny19

src/get_primary_sam.py

@@ -365,6 +365,10 @@ def primary_and_unaligned_chimeric(sam_alnm_file, prefix, metagenome_list=None,
                 continue
             beta_list.append(counts[1] / (counts[0] + counts[1]) * 100 / other_prob)
 
+    strandness = float(pos_strand) / num_aligned
+    if q_mode:
+        return [], strandness
+
     out_sam_file.close()
     unaligned_len = numpy.array(unaligned_len)
 
@@ -382,8 +386,4 @@ def primary_and_unaligned_chimeric(sam_alnm_file, prefix, metagenome_list=None,
         chimeric_file.write("Shrinkage rate (beta):\t" + str(median(beta_list)))
     chimeric_file.close()
 
-    strandness = float(pos_strand) / num_aligned
-    if q_mode:
-        return [], strandness
-
     return unaligned_len, strandness

src/read_analysis.py

@@ -253,7 +253,7 @@ def main():
     parser_t = subparsers.add_parser('transcriptome', help="Run the simulator on transcriptome mode")
     parser_t.add_argument('-i', '--read', help='Input read for training', required=True)
     parser_t.add_argument('-rg', '--ref_g', help='Reference genome', required=True)
-    parser_t.add_argument('-rt', '--ref_t', help='Reference Transcriptome', required=True)  # ?
+    parser_t.add_argument('-rt', '--ref_t', help='Reference Transcriptome', required=True)
     parser_t.add_argument('-annot', '--annotation', help='Annotation file in ensemble GTF/GFF formats, '
                                                          'required for intron retention detection', default='')
     parser_t.add_argument('-a', '--aligner', help='The aligner to be used: minimap2 or LAST (Default = minimap2)',