don't count clipped regions in the length_on_ref for BAM alignments, references #229
don't count clipped regions in the length_on_ref for BAM alignments, references #229

limeng12/jbrowse,erasche/jbrowse,erasche/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,igemsoftware/Shenzhen_BGIC_0101_2013,SuLab/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,limeng12/jbrowse,erasche/jbrowse,SuLab/jbrowse,Arabidopsis-Information-Portal/jbrowse,SuLab/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,Arabidopsis-Information-Portal/jbrowse,limeng12/jbrowse,nathandunn/jbrowse,GMOD/jbrowse,erasche/jbrowse,erasche/jbrowse,limeng12/jbrowse,erasche/jbrowse,SuLab/jbrowse,nathandunn/jbrowse,nathandunn/jbrowse,GMOD/jbrowse,erasche/jbrowse,limeng12/jbrowse,Arabidopsis-Information-Portal/jbrowse,GMOD/jbrowse,limeng12/jbrowse,SuLab/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,igemsoftware/Shenzhen_BGIC_0101_2013,limeng12/jbrowse,SuLab/jbrowse,erasche/jbrowse,nathandunn/jbrowse,Arabidopsis-Information-Portal/jbrowse,Arabidopsis-Information-Portal/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,Arabidopsis-Information-Portal/jbrowse,SuLab/jbrowse,GMOD/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,limeng12/jbrowse,Arabidopsis-Information-Portal/jbrowse,GMOD/jbrowse,nathandunn/jbrowse