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# Line 2238 | Line 2238
2238                  seg = read_segments[i]
2239                  fbasename=getFileBaseName(seg)
2240                  seg_out =  tmp_dir + fbasename + ".mapped"
2241 <                if use_zpacker: seg_out += ".z"
2241 >                #if use_zpacker: seg_out += ".z"
2242                  unmapped_seg = tmp_dir + fbasename + "_unmapped"
2243                  extra_output = "(%d/%d)" % (i+1, len(read_segments))
2244                  (seg_map, unmapped) = bowtie_segment(params,
# Line 2346 | Line 2346
2346              i = 0
2347              for seg in maps[reads].segs:
2348                  fsegname = getFileBaseName(seg)
2349 <                seg_out = tmp_dir + fsegname + ".to_spliced.bwtout"
2350 <                if use_zpacker: seg_out += ".z"
2349 >                seg_out = tmp_dir + fsegname + ".to_spliced"
2350 >                #if use_zpacker: seg_out += ".z"
2351                  extra_output = "(%d/%d)" % (i+1, len(maps[reads].segs))
2352                  (seg_map, unmapped) = bowtie_segment(params,
2353                                                       tmp_dir + junc_idx_prefix,

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