- a -

• AUX_FIRST_MARKER_COL : options.c
• AUX_INPUT_FNAME : options.c
• AUX_LABEL_COL : options.c
• AUX_NUM_MARKERS : options.c

- b -

• BMM_CONF_THRESH_FNAME : options.c
• BMM_INFO_FNAME : options.c
• BMM_TREE_FNAME : options.c

- c -

• CLUSTER_TYPE : haplo_cluster.c

- d -

• DATA_OUT_DIRNAME : haplo_train.c

- e -

• EXCLUDE_ONE : options.c

- f -

• FIRST_MARKER_COL : options.c

- g -

• GMM_BMM_CONF_THRESH_FNAME : options.c
• GMM_BMM_INFO_FNAME : options.c
• GMM_BMM_TREE_FNAME : options.c

- h -

• HEADER_IN : options.c
• HEADER_OUT : options.c

- i -

• INPUT_DTD_FNAME : options.c
• INPUT_FORMAT : options.c

- l -

• LABEL_COL : haplo_cluster.c , haplo_train.c , haplo_test.c , haplo_predict.c
• LABELS_DTD_FNAME : options.c
• LABELS_FNAME : options.c

- m -

• MAX_COL_SIZE : input.c
• MEANS_OUT_FNAME : haplo_cluster.c
• MEMBERS_OUT_FNAME : haplo_cluster.c
• MODEL_DIRNAME : options.c
• MV_GMM_CONFUSION_CNT_FNAME : haplo_test.c
• MV_GMM_CONFUSION_PCT_FNAME : haplo_test.c
• MV_GMM_DETAILS_CNT_FNAME : haplo_test.c
• MV_GMM_DETAILS_PCT_FNAME : haplo_test.c
• MV_GMM_DTD_FNAME : options.c
• MV_GMM_FNAME : options.c
• MV_GMM_PREDS_FNAME : haplo_test.c
• MV_GMM_SUMMARY_FNAME : haplo_test.c
• MV_MMM_DTD_FNAME : options.c
• MV_MMM_FNAME : options.c

- n -

• NB_FREQ_CONFUSION_CNT_FNAME : haplo_test.c
• NB_FREQ_CONFUSION_PCT_FNAME : haplo_test.c
• NB_FREQ_DETAILS_CNT_FNAME : haplo_test.c
• NB_FREQ_DETAILS_PCT_FNAME : haplo_test.c
• NB_FREQ_DTD_FNAME : options.c
• NB_FREQ_FNAME : options.c
• NB_FREQ_PREDS_FNAME : haplo_test.c
• NB_FREQ_SUMMARY_FNAME : haplo_test.c
• NB_GAUSS_CONFUSION_CNT_FNAME : haplo_test.c
• NB_GAUSS_CONFUSION_PCT_FNAME : haplo_test.c
• NB_GAUSS_DETAILS_CNT_FNAME : haplo_test.c
• NB_GAUSS_DETAILS_PCT_FNAME : haplo_test.c
• NB_GAUSS_DTD_FNAME : options.c
• NB_GAUSS_FNAME : options.c
• NB_GAUSS_PREDS_FNAME : haplo_test.c
• NB_GAUSS_SUMMARY_FNAME : haplo_test.c
• NB_GMM_CONFUSION_CNT_FNAME : haplo_test.c
• NB_GMM_CONFUSION_PCT_FNAME : haplo_test.c
• NB_GMM_DETAILS_CNT_FNAME : haplo_test.c
• NB_GMM_DETAILS_PCT_FNAME : haplo_test.c
• NB_GMM_DTD_FNAME : options.c
• NB_GMM_FNAME : options.c
• NB_GMM_PREDS_FNAME : haplo_test.c
• NB_GMM_SUMMARY_FNAME : haplo_test.c
• NEAREST_CONFUSION_CNT_FNAME : haplo_test.c
• NEAREST_CONFUSION_PCT_FNAME : haplo_test.c
• NEAREST_DETAILS_CNT_FNAME : haplo_test.c
• NEAREST_DETAILS_PCT_FNAME : haplo_test.c
• NEAREST_DTD_FNAME : options.c
• NEAREST_FNAME : options.c
• NEAREST_MAX_D : options.c
• NEAREST_PREDS_FNAME : haplo_test.c
• NEAREST_SUMMARY_FNAME : haplo_test.c
• NUM_ALGOS : haplo_predict.c
• NUM_CLUSTERS : haplo_cluster.c
• NUM_CV_FOLDS : haplo_test.c
• NUM_CV_ITERS : haplo_test.c
• NUM_MARKERS : options.c
• NUM_OPTS_NO_ARG : haplo_test.c , haplo_cluster.c , haplo_train.c , haplo_predict.c
• NUM_OPTS_WITH_ARG : haplo_train.c , haplo_cluster.c , haplo_test.c , haplo_predict.c
• NUM_SHARED_OPTS_NO_ARG : options.h
• NUM_SHARED_OPTS_WITH_ARG : options.h
• NUM_SVM_OPTS : haplo_predict.c , haplo_train.c , haplo_test.c
• NUM_THREAD_OPTS : options.h
• NUM_THREADS : options.c
• NUM_WEKA_OPTS : haplo_train.c , haplo_test.c , haplo_predict.c

- o -

• OUTPUT_FNAME : haplo_predict.c
• OUTPUT_FORMAT : options.c

- r -

• RESPONSES_OUT_FNAME : haplo_cluster.c

- s -

• SVM_CONFUSION_CNT_FNAME : haplo_test.c
• SVM_CONFUSION_PCT_FNAME : haplo_test.c
• SVM_DETAILS_CNT_FNAME : haplo_test.c
• SVM_DETAILS_PCT_FNAME : haplo_test.c
• SVM_DTD_FNAME : options.c
• SVM_FNAME : options.c
• SVM_PREDS_FNAME : haplo_test.c
• SVM_SUMMARY_FNAME : haplo_test.c

- t -

• TANDEM : haplo_test.c
• TANDEM_AGREE_DETAILS_CNT_FNAME : haplo_test.c
• TANDEM_AGREE_DETAILS_PCT_FNAME : haplo_test.c
• TANDEM_AGREE_SUMMARY_FNAME : haplo_test.c
• TANDEM_CONFUSION_CNT_FNAME : haplo_test.c
• TANDEM_CONFUSION_PCT_FNAME : haplo_test.c
• TANDEM_DETAILS_CNT_FNAME : haplo_test.c
• TANDEM_DETAILS_PCT_FNAME : haplo_test.c
• TANDEM_PREDS_FNAME : haplo_test.c
• TANDEM_SUMMARY_FNAME : haplo_test.c
• TEST_TYPE : haplo_test.c
• TMP_DIRNAME : haplo_test.c

- w -

• WEIGHTS_OUT_FNAME : haplo_cluster.c
• WEKA_DTD_FNAME : options.c
• WEKA_J48_CONFUSION_CNT_FNAME : haplo_test.c
• WEKA_J48_CONFUSION_PCT_FNAME : haplo_test.c
• WEKA_J48_DETAILS_CNT_FNAME : haplo_test.c
• WEKA_J48_DETAILS_PCT_FNAME : haplo_test.c
• WEKA_J48_FNAME : options.c
• WEKA_J48_PREDS_FNAME : haplo_test.c
• WEKA_J48_SUMMARY_FNAME : haplo_test.c
• WEKA_JAR_FNAME : options.c
• WEKA_PART_CONFUSION_CNT_FNAME : haplo_test.c
• WEKA_PART_CONFUSION_PCT_FNAME : haplo_test.c
• WEKA_PART_DETAILS_CNT_FNAME : haplo_test.c
• WEKA_PART_DETAILS_PCT_FNAME : haplo_test.c
• WEKA_PART_FNAME : options.c
• WEKA_PART_PREDS_FNAME : haplo_test.c
• WEKA_PART_SUMMARY_FNAME : haplo_test.c

- x -

• XMLCreateIntSubset : xml.h
• XMLNewChild : xml.h
• XMLNewNode : xml.h
• XMLNewProp : xml.h
• XMLStrEqual : xml.h