generates the index file using the latest java index generating code concode_field_sep File BAI_FILE concode_elem_sep String BAM_FILE_LOCATION concode_elem_sep String BAI_FILE_LOCATION concode_elem_sep File BAM_FILE concode_elem_sep boolean mVerbose concode_field_sep void testWriteBinary concode_elem_sep Object[][] getIndexComparisonData concode_elem_sep Object[][] getLinearIndexTestData concode_elem_sep void testLinearIndex concode_elem_sep void compareLinearIndex concode_elem_sep void testWriteText concode_elem_sep int countAlignmentsInWindow concode_elem_sep void verbose
File function ( File arg0 ) { final File loc0 = File . createTempFile ( "srini_string" , "srini_string" ) ; final SamReader loc1 = SamReaderFactory . makeDefault ( ) . open ( arg0 ) ; BAMIndexer . createIndex ( loc1 , loc0 ) ; verbose ( "srini_string" + loc0 ) ; loc1 . close ( ) ; return loc0 ; }