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Bob Harris committed 8a4101f

recommitting earlier change, involving correction of how intervals are handled on negative strand

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scripts/maf_extract_ranges.py

 
     for maf in bx.align.maf.Reader( sys.stdin ):
         ref_component = maf.components[ refindex ]
+        if ref_component.strand == '-':
+            maf = maf.reverse_complement()
+            ref_component = maf.components[ refindex ]
         # Find overlap with reference component
         intersections = intersecter.find( ref_component.start, ref_component.end )
         # Keep output maf ordered