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# Line 622 | Line 622
622  
623          self.keep_fasta_order = False
624          self.partial_mapping = False
625 <        
625 >
626          self.fusion_search = False
627          self.fusion_anchor_length = 20
628          self.fusion_min_dist = 10000000
# Line 1174 | Line 1174
1174      try:
1175          temp_sam_header_filename = tmp_dir + "temp.samheader.sam"
1176          temp_sam_header_file = open(temp_sam_header_filename, "w")
1177 <        
1177 >
1178          bowtie_header_cmd = [bowtie_path]
1179  
1180          read_params = params.read_params
# Line 1240 | Line 1240
1240  
1241          if not params.keep_fasta_order:
1242              sq_dict_lines.sort(lambda x,y: cmp(x[0],y[0]))
1243 <            
1243 >
1244          for [name, line] in sq_dict_lines:
1245              print >> bowtie_sam_header_file, line
1246          print >> bowtie_sam_header_file, "@PG\tID:TopHat\tVN:%s\tCL:%s" % (get_version(), run_cmd)
# Line 1892 | Line 1892
1892                  max_penalty, min_penalty = int(max_penalty), int(min_penalty)
1893                  min_score = (max_penalty - 1) * num_mismatches
1894                  fix_map_cmd += ["--bowtie2-min-score", str(min_score)]
1895 <            
1895 >
1896          samzip_cmd=None
1897  
1898          # daehwan - just use bam format for multi-threading.
# Line 1928 | Line 1928
1928              max_hits = params.max_seg_hits
1929          else:
1930              max_hits = params.max_hits
1931 <            
1931 >
1932          if num_mismatches > 3:
1933             num_mismatches = 3
1934  
# Line 2308 | Line 2308
2308      report_cmd += ["--sam-header", sam_header_filename]
2309      if params.report_secondary_alignments:
2310          report_cmd += ["--report-secondary-alignments"]
2311 <    
2311 >
2312      report_cmd.extend(["--samtools="+samtools_path])
2313      report_cmd.extend([ref_fasta,
2314                         junctions,
# Line 2846 | Line 2846
2846         m2g_bwt_idx = build_idx_from_fa(params.bowtie2, m2g_ref_fasta, t_out_dir, params.read_params.color)
2847  
2848      get_index_sam_header(params, m2g_bwt_idx)
2849 <    
2849 >
2850      mapped_gtf_list = []
2851      unmapped_gtf_list = []
2852      # do the initial mapping in GTF coordinates
# Line 3444 | Line 3444
3444              (found_juncs, gtf_juncs) = get_gtf_juncs(params.gff_annotation)
3445              ##-- we shouldn't need these junctions in user_supplied_juncs anymore because now map2gtf does a much better job
3446              ## but we still need them loaded in gtf_juncs for later splice verification
3447 <            if found_juncs:
3447 >            if found_juncs:
3448                  ## and not params.gff_annotation:
3449                  user_supplied_juncs.append(gtf_juncs)
3450              #else:

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