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byte-store.c
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byte-store.c
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#include "byte-store.h"
int
main(int argc, char** argv)
{
bs_init_globals();
bs_init_command_line_options(argc, argv);
sut_store_t* sut_store = NULL;
sqr_store_t* sqr_store = NULL;
lookup_t* lookup = NULL;
/* initialize lookup table */
if ((bs_globals.store_type == kStorePearsonRSquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata) ||
(bs_globals.store_type == kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata)) {
lookup = bs_init_lookup(bs_globals.lookup_fn,
kFalse,
kFalse,
kFalse);
}
else if ((bs_globals.store_type == kStorePearsonRSquareMatrix) ||
(bs_globals.store_type == kStorePearsonRSquareMatrixSplit) ||
(bs_globals.store_type == kStorePearsonRSquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStorePearsonRSquareMatrixBzip2) ||
(bs_globals.store_type == kStorePearsonRSquareMatrixBzip2Split) ||
(bs_globals.store_type == kStoreNormalizedEuclideanDistanceSquareMatrix) ||
(bs_globals.store_type == kStoreNormalizedEuclideanDistanceSquareMatrixSplit) ||
(bs_globals.store_type == kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStoreCosineSimilaritySquareMatrix) ||
(bs_globals.store_type == kStoreCosineSimilaritySquareMatrixSplit) ||
(bs_globals.store_type == kStoreCosineSimilaritySquareMatrixSplitSingleChunk)) {
lookup = bs_init_lookup(bs_globals.lookup_fn,
!bs_globals.store_query_flag && !bs_globals.store_frequency_flag,
((bs_globals.store_frequency_flag) ? kFalse : kTrue),
kFalse);
}
else if (((bs_globals.store_type == kStoreSpearmanRhoSquareMatrix) ||
(bs_globals.store_type == kStoreSpearmanRhoSquareMatrixSplit) ||
(bs_globals.store_type == kStoreSpearmanRhoSquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStoreSpearmanRhoSquareMatrixBzip2) ||
(bs_globals.store_type == kStoreSpearmanRhoSquareMatrixBzip2Split)) &&
(!bs_globals.store_query_daemon_flag)) {
lookup = bs_init_lookup(bs_globals.lookup_fn,
!bs_globals.store_query_flag && !bs_globals.store_frequency_flag,
((bs_globals.store_frequency_flag) ? kFalse : kTrue),
kTrue);
}
else if ((bs_globals.store_type == kStoreJaccardIndexSquareMatrix) ||
(bs_globals.store_type == kStoreJaccardIndexSquareMatrixSplit) ||
(bs_globals.store_type == kStoreJaccardIndexSquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStoreOchiaiSimilaritySquareMatrix) ||
(bs_globals.store_type == kStoreOchiaiSimilaritySquareMatrixSplit) ||
(bs_globals.store_type == kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStorePearsonPhiSimilaritySquareMatrix) ||
(bs_globals.store_type == kStorePearsonPhiSimilaritySquareMatrixSplit) ||
(bs_globals.store_type == kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStoreRogersAndTanimotoSimilaritySquareMatrix) ||
(bs_globals.store_type == kStoreRogersAndTanimotoSimilaritySquareMatrixSplit) ||
(bs_globals.store_type == kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk) ||
(bs_globals.store_type == kStoreNormalizedPointwiseMutualInformationSquareMatrix) ||
(bs_globals.store_type == kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit) ||
(bs_globals.store_type == kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk)) {
lookup = bs_init_lookup(bs_globals.lookup_fn,
!bs_globals.store_query_flag,
kFalse,
kFalse);
}
else if (bs_globals.store_query_daemon_flag) {
lookup = bs_init_lookup(bs_globals.lookup_fn,
kFalse,
kFalse,
kFalse);
}
else {
lookup = bs_init_lookup(bs_globals.lookup_fn,
!bs_globals.store_query_flag,
kFalse,
kFalse);
}
/* create or query byte-store container */
switch (bs_globals.store_type) {
case kStorePearsonRSUT:
case kStoreRandomSUT:
sut_store = bs_init_sut_store(lookup->nelems);
if (bs_globals.store_create_flag) {
switch (bs_globals.store_type) {
case kStoreRandomSUT:
bs_populate_sut_store_with_random_scores(sut_store);
break;
case kStorePearsonRSUT:
bs_populate_sut_store(sut_store,
lookup,
&bs_pearson_r_signal);
break;
case kStoreRandomBufferedSquareMatrix:
case kStoreRandomSquareMatrix:
case kStorePearsonRSquareMatrix:
case kStorePearsonRSquareMatrixSplit:
case kStorePearsonRSquareMatrixSplitSingleChunk:
case kStorePearsonRSquareMatrixSplitSingleChunkMetadata:
case kStorePearsonRSquareMatrixBzip2:
case kStorePearsonRSquareMatrixBzip2Split:
case kStoreSpearmanRhoSquareMatrix:
case kStoreSpearmanRhoSquareMatrixSplit:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunk:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata:
case kStoreSpearmanRhoSquareMatrixBzip2:
case kStoreSpearmanRhoSquareMatrixBzip2Split:
case kStoreNormalizedEuclideanDistanceSquareMatrix:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplit:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata:
case kStoreCosineSimilaritySquareMatrix:
case kStoreCosineSimilaritySquareMatrixSplit:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunk:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreJaccardIndexSquareMatrix:
case kStoreJaccardIndexSquareMatrixSplit:
case kStoreJaccardIndexSquareMatrixSplitSingleChunk:
case kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata:
case kStoreOchiaiSimilaritySquareMatrix:
case kStoreOchiaiSimilaritySquareMatrixSplit:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStorePearsonPhiSimilaritySquareMatrix:
case kStorePearsonPhiSimilaritySquareMatrixSplit:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreRogersAndTanimotoSimilaritySquareMatrix:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplit:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedPointwiseMutualInformationSquareMatrix:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata:
case kStoreUndefined:
fprintf(stderr, "Error: You should never see this error! (A)\n");
exit(EXIT_FAILURE);
}
}
else if (bs_globals.store_query_flag && !bs_globals.store_query_daemon_flag) {
boolean_t rows_found = kFalse;
switch (bs_globals.store_query_kind) {
case kQueryKindIndex:
rows_found = bs_parse_query_index_str(lookup);
break;
case kQueryKindRange:
rows_found = bs_parse_query_range_str(lookup,
bs_globals.store_query_str,
&bs_globals.store_query_idx_start,
&bs_globals.store_query_idx_end);
break;
case kQueryKindMultipleIndices:
case kQueryKindMultipleIndicesFromFile:
case kQueryKindMultipleRowAndColumnIndicesFromFile:
case kQueryKindDiagonalOffset:
case kQueryKindUndefined:
fprintf(stderr, "Error: Query type unsupported with SUT!\n");
exit(EXIT_FAILURE);
}
if (rows_found && (bs_globals.store_filter == kScoreFilterNone))
bs_print_sut_store_to_bed7(lookup,
sut_store,
stdout);
else if (rows_found)
bs_print_sut_filtered_store_to_bed7(lookup,
sut_store,
stdout,
bs_globals.score_filter_cutoff,
bs_globals.store_filter);
}
else if (bs_globals.store_frequency_flag) {
bs_print_sut_frequency_to_txt(lookup,
sut_store,
stdout);
}
bs_delete_sut_store(&sut_store);
break;
case kStorePearsonRSquareMatrix:
case kStorePearsonRSquareMatrixSplit:
case kStorePearsonRSquareMatrixSplitSingleChunk:
case kStorePearsonRSquareMatrixSplitSingleChunkMetadata:
case kStorePearsonRSquareMatrixBzip2:
case kStorePearsonRSquareMatrixBzip2Split:
case kStoreSpearmanRhoSquareMatrix:
case kStoreSpearmanRhoSquareMatrixSplit:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunk:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata:
case kStoreSpearmanRhoSquareMatrixBzip2:
case kStoreSpearmanRhoSquareMatrixBzip2Split:
case kStoreNormalizedEuclideanDistanceSquareMatrix:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplit:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata:
case kStoreCosineSimilaritySquareMatrix:
case kStoreCosineSimilaritySquareMatrixSplit:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunk:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreJaccardIndexSquareMatrix:
case kStoreJaccardIndexSquareMatrixSplit:
case kStoreJaccardIndexSquareMatrixSplitSingleChunk:
case kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata:
case kStoreOchiaiSimilaritySquareMatrix:
case kStoreOchiaiSimilaritySquareMatrixSplit:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStorePearsonPhiSimilaritySquareMatrix:
case kStorePearsonPhiSimilaritySquareMatrixSplit:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreRogersAndTanimotoSimilaritySquareMatrix:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplit:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedPointwiseMutualInformationSquareMatrix:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata:
case kStoreRandomSquareMatrix:
case kStoreRandomBufferedSquareMatrix:
sqr_store = bs_init_sqr_store(lookup->nelems);
if (bs_globals.store_create_flag) {
switch (bs_globals.store_type) {
case kStoreRandomBufferedSquareMatrix:
bs_populate_sqr_store_with_buffered_random_scores(sqr_store);
break;
case kStoreRandomSquareMatrix:
bs_populate_sqr_store_with_random_scores(sqr_store);
break;
case kStorePearsonRSquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_pearson_r_signal);
break;
case kStorePearsonRSquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_pearson_r_signal,
kScoreVarietyPearsonR);
break;
case kStorePearsonRSquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_pearson_r_signal);
break;
case kStorePearsonRSquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyPearsonR);
break;
case kStorePearsonRSquareMatrixBzip2:
bs_populate_sqr_bzip2_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_pearson_r_signal,
kScoreVarietyPearsonR);
break;
case kStorePearsonRSquareMatrixBzip2Split:
bs_populate_sqr_bzip2_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_pearson_r_signal,
kScoreVarietyPearsonR);
break;
case kStoreSpearmanRhoSquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_spearman_rho_signal_v2);
break;
case kStoreSpearmanRhoSquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_spearman_rho_signal_v2,
kScoreVarietySpearmanRho);
break;
case kStoreSpearmanRhoSquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_spearman_rho_signal_v2);
break;
case kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietySpearmanRho);
break;
case kStoreSpearmanRhoSquareMatrixBzip2:
bs_populate_sqr_bzip2_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_spearman_rho_signal_v2,
kScoreVarietySpearmanRho);
break;
case kStoreSpearmanRhoSquareMatrixBzip2Split:
bs_populate_sqr_bzip2_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_spearman_rho_signal_v2,
kScoreVarietySpearmanRho);
break;
case kStoreNormalizedEuclideanDistanceSquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_normalized_euclidean_distance_signal);
break;
case kStoreNormalizedEuclideanDistanceSquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_normalized_euclidean_distance_signal,
kScoreVarietyNormalizedEuclideanDistance);
break;
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_normalized_euclidean_distance_signal);
break;
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyNormalizedEuclideanDistance);
break;
case kStoreCosineSimilaritySquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_cosine_similarity_signal);
break;
case kStoreCosineSimilaritySquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_cosine_similarity_signal,
kScoreVarietyCosineSimilarity);
break;
case kStoreCosineSimilaritySquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_cosine_similarity_signal);
break;
case kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyCosineSimilarity);
break;
case kStoreJaccardIndexSquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_jaccard_index_signal);
break;
case kStoreJaccardIndexSquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_jaccard_index_signal,
kScoreVarietyJaccardIndex);
break;
case kStoreJaccardIndexSquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_jaccard_index_signal);
break;
case kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyJaccardIndex);
break;
case kStoreOchiaiSimilaritySquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_ochiai_similarity_signal);
break;
case kStoreOchiaiSimilaritySquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_ochiai_similarity_signal,
kScoreVarietyOchiaiSimilarity);
break;
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_ochiai_similarity_signal);
break;
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyOchiaiSimilarity);
break;
case kStorePearsonPhiSimilaritySquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_pearson_phi_similarity_signal);
break;
case kStorePearsonPhiSimilaritySquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_pearson_phi_similarity_signal,
kScoreVarietyPearsonPhiSimilarity);
break;
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_pearson_phi_similarity_signal);
break;
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyPearsonPhiSimilarity);
break;
case kStoreRogersAndTanimotoSimilaritySquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_rogers_and_tanimoto_similarity_signal);
break;
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_rogers_and_tanimoto_similarity_signal,
kScoreVarietyRogersAndTanimotoSimilarity);
break;
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_rogers_and_tanimoto_similarity_signal);
break;
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyRogersAndTanimotoSimilarity);
break;
case kStoreNormalizedPointwiseMutualInformationSquareMatrix:
bs_populate_sqr_store(sqr_store,
lookup,
&bs_normalized_pointwise_mutual_information_signal);
break;
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit:
bs_populate_sqr_split_store(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
&bs_normalized_pointwise_mutual_information_signal,
kScoreVarietyNormalizedPointwiseMutualInformation);
break;
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk:
bs_populate_sqr_split_store_chunk(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
bs_globals.store_row_chunk_offset,
&bs_normalized_pointwise_mutual_information_signal);
break;
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata:
bs_populate_sqr_split_store_chunk_metadata(sqr_store,
lookup,
bs_globals.store_row_chunk_size,
kScoreVarietyNormalizedPointwiseMutualInformation);
break;
case kStorePearsonRSUT:
case kStoreRandomSUT:
case kStoreUndefined:
fprintf(stderr, "Error: You should never see this error! (B)\n");
exit(EXIT_FAILURE);
}
}
else if (bs_globals.store_query_flag && !bs_globals.store_query_daemon_flag) {
/* set up query type */
boolean_t contiguous_rows_found = kFalse;
boolean_t separate_rows_found = kFalse;
switch (bs_globals.store_query_kind) {
case kQueryKindIndex:
contiguous_rows_found = bs_parse_query_index_str(lookup);
break;
case kQueryKindRange:
contiguous_rows_found = bs_parse_query_range_str(lookup,
bs_globals.store_query_str,
&bs_globals.store_query_idx_start,
&bs_globals.store_query_idx_end);
break;
case kQueryKindMultipleIndices:
separate_rows_found = bs_parse_query_multiple_index_str(lookup,
bs_globals.store_query_str);
break;
case kQueryKindMultipleIndicesFromFile:
separate_rows_found = bs_parse_query_multiple_index_file(lookup,
bs_globals.store_query_str);
break;
case kQueryKindMultipleRowAndColumnIndicesFromFile:
case kQueryKindDiagonalOffset:
separate_rows_found = kTrue;
break;
case kQueryKindUndefined:
fprintf(stderr, "Error: Query type unsupported!\n");
exit(EXIT_FAILURE);
}
if (contiguous_rows_found) {
if (bs_globals.store_query_idx_end < bs_globals.store_query_idx_start) {
fprintf(stderr, "Error: Query index bounds not ordered\n");
exit(EXIT_FAILURE);
}
size_t query_roi_num = 1;
size_t* query_roi_start = malloc(sizeof(*query_roi_start));
size_t* query_roi_end = malloc(sizeof(*query_roi_end));
query_roi_start[0] = bs_globals.store_query_idx_start;
query_roi_end[0] = bs_globals.store_query_idx_end;
/* extract from raw or uncompressed square matrix */
switch (bs_globals.store_type) {
case kStoreRandomBufferedSquareMatrix:
case kStoreRandomSquareMatrix:
case kStorePearsonRSquareMatrix:
case kStoreSpearmanRhoSquareMatrix:
case kStoreNormalizedEuclideanDistanceSquareMatrix:
case kStoreCosineSimilaritySquareMatrix:
case kStoreJaccardIndexSquareMatrix:
case kStoreOchiaiSimilaritySquareMatrix:
case kStorePearsonPhiSimilaritySquareMatrix:
case kStoreRogersAndTanimotoSimilaritySquareMatrix:
case kStoreNormalizedPointwiseMutualInformationSquareMatrix:
if (bs_globals.store_filter == kScoreFilterNone)
bs_print_sqr_store_to_bed7(lookup,
sqr_store,
bs_globals.store_filter_mutual_set,
stdout,
bs_globals.store_query_idx_start,
bs_globals.store_query_idx_end);
else
bs_print_sqr_filtered_store_to_bed7(lookup,
sqr_store,
bs_globals.store_filter_mutual_set,
stdout,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter,
bs_globals.store_query_idx_start,
bs_globals.store_query_idx_end);
break;
case kStorePearsonRSquareMatrixSplit:
case kStoreSpearmanRhoSquareMatrixSplit:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplit:
case kStoreCosineSimilaritySquareMatrixSplit:
case kStoreJaccardIndexSquareMatrixSplit:
case kStoreOchiaiSimilaritySquareMatrixSplit:
case kStorePearsonPhiSimilaritySquareMatrixSplit:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplit:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit:
if (bs_globals.store_filter == kScoreFilterNone) {
bs_print_sqr_split_store_separate_rows_to_bed7(lookup,
sqr_store,
bs_globals.store_filter_mutual_set,
stdout,
query_roi_start,
query_roi_end,
query_roi_num);
}
else {
bs_print_sqr_filtered_split_store_separate_rows_to_bed7(lookup,
sqr_store,
bs_globals.store_filter_mutual_set,
stdout,
query_roi_start,
query_roi_end,
query_roi_num,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
}
break;
case kStorePearsonRSquareMatrixBzip2:
case kStoreSpearmanRhoSquareMatrixBzip2:
if (bs_globals.store_filter == kScoreFilterNone)
bs_print_sqr_bzip2_store_to_bed7(lookup,
sqr_store,
stdout);
else
bs_print_sqr_filtered_bzip2_store_to_bed7(lookup,
sqr_store,
stdout,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
break;
case kStorePearsonRSquareMatrixBzip2Split:
case kStoreSpearmanRhoSquareMatrixBzip2Split:
if (bs_globals.store_filter == kScoreFilterNone)
bs_print_sqr_bzip2_split_store_to_bed7(lookup,
sqr_store,
stdout);
else
bs_print_sqr_filtered_bzip2_split_store_to_bed7(lookup,
sqr_store,
stdout,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
break;
case kStorePearsonRSUT:
case kStoreRandomSUT:
case kStorePearsonRSquareMatrixSplitSingleChunk:
case kStorePearsonRSquareMatrixSplitSingleChunkMetadata:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunk:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunk:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreJaccardIndexSquareMatrixSplitSingleChunk:
case kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata:
case kStoreUndefined:
fprintf(stderr, "Error: You should never see this error! (C1)\n");
exit(EXIT_FAILURE);
}
/* clean-up */
free(query_roi_start);
free(query_roi_end);
query_roi_start = NULL;
query_roi_end = NULL;
}
if (separate_rows_found) {
switch (bs_globals.store_type) {
case kStorePearsonRSquareMatrixSplit:
case kStoreSpearmanRhoSquareMatrixSplit:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplit:
case kStoreCosineSimilaritySquareMatrixSplit:
case kStoreJaccardIndexSquareMatrixSplit:
case kStoreOchiaiSimilaritySquareMatrixSplit:
case kStorePearsonPhiSimilaritySquareMatrixSplit:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplit:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit:
switch (bs_globals.store_query_kind) {
case kQueryKindMultipleRowAndColumnIndicesFromFile:
if (bs_globals.store_filter == kScoreFilterNone) {
bs_print_sqr_split_store_separate_rows_and_columns_to_bed7_file(lookup,
sqr_store,
bs_globals.store_query_str,
stdout);
}
else {
bs_print_sqr_filtered_split_store_separate_rows_and_columns_to_bed7_file(lookup,
sqr_store,
bs_globals.store_query_str,
stdout,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
}
break;
case kQueryKindMultipleIndicesFromFile:
if (bs_globals.store_filter == kScoreFilterNone) {
bs_print_sqr_split_store_separate_rows_to_bed7_file(lookup,
sqr_store,
bs_globals.store_query_str,
bs_globals.store_filter_mutual_set,
stdout);
}
else {
bs_print_sqr_filtered_split_store_separate_rows_to_bed7_file(lookup,
sqr_store,
bs_globals.store_query_str,
bs_globals.store_filter_mutual_set,
stdout,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
}
break;
case kQueryKindDiagonalOffset:
if (bs_globals.store_filter == kScoreFilterNone) {
bs_print_sqr_split_diagonal_walk_fixed_distance(lookup,
sqr_store,
stdout,
bs_globals.diagonal_offset_value,
bs_globals.diagonal_offset_side);
}
else {
bs_print_sqr_filtered_split_diagonal_walk_fixed_distance(lookup,
sqr_store,
stdout,
bs_globals.diagonal_offset_value,
bs_globals.diagonal_offset_side,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
}
break;
default:
if (bs_globals.store_filter == kScoreFilterNone) {
bs_print_sqr_split_store_separate_rows_to_bed7(lookup,
sqr_store,
bs_globals.store_filter_mutual_set,
stdout,
bs_globals.store_query_indices_starts,
bs_globals.store_query_indices_ends,
bs_globals.store_query_indices_num);
}
else {
bs_print_sqr_filtered_split_store_separate_rows_to_bed7(lookup,
sqr_store,
bs_globals.store_filter_mutual_set,
stdout,
bs_globals.store_query_indices_starts,
bs_globals.store_query_indices_ends,
bs_globals.store_query_indices_num,
bs_globals.score_filter_cutoff,
bs_globals.score_filter_cutoff_lower_bound,
bs_globals.score_filter_cutoff_upper_bound,
bs_globals.store_filter);
}
break;
}
break;
case kStoreRandomBufferedSquareMatrix:
case kStoreRandomSquareMatrix:
case kStorePearsonRSquareMatrix:
case kStorePearsonRSquareMatrixSplitSingleChunk:
case kStorePearsonRSquareMatrixSplitSingleChunkMetadata:
case kStorePearsonRSquareMatrixBzip2:
case kStorePearsonRSquareMatrixBzip2Split:
case kStorePearsonRSUT:
case kStoreSpearmanRhoSquareMatrix:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunk:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata:
case kStoreSpearmanRhoSquareMatrixBzip2:
case kStoreSpearmanRhoSquareMatrixBzip2Split:
case kStoreNormalizedEuclideanDistanceSquareMatrix:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata:
case kStoreCosineSimilaritySquareMatrix:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunk:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreJaccardIndexSquareMatrix:
case kStoreJaccardIndexSquareMatrixSplitSingleChunk:
case kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata:
case kStoreOchiaiSimilaritySquareMatrix:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStorePearsonPhiSimilaritySquareMatrix:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreRogersAndTanimotoSimilaritySquareMatrix:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedPointwiseMutualInformationSquareMatrix:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata:
case kStoreRandomSUT:
case kStoreUndefined:
fprintf(stderr, "Error: You should never see this error! (C2)\n");
exit(EXIT_FAILURE);
}
}
}
else if (bs_globals.store_frequency_flag) {
switch (bs_globals.store_type) {
case kStoreRandomBufferedSquareMatrix:
case kStoreRandomSquareMatrix:
case kStorePearsonRSquareMatrix:
case kStoreSpearmanRhoSquareMatrix:
case kStoreJaccardIndexSquareMatrix:
case kStoreNormalizedEuclideanDistanceSquareMatrix:
case kStoreCosineSimilaritySquareMatrix:
case kStoreOchiaiSimilaritySquareMatrix:
case kStorePearsonPhiSimilaritySquareMatrix:
case kStoreRogersAndTanimotoSimilaritySquareMatrix:
case kStoreNormalizedPointwiseMutualInformationSquareMatrix:
bs_print_sqr_store_frequency_to_txt(lookup,
sqr_store,
stdout);
break;
case kStorePearsonRSquareMatrixSplit:
case kStoreSpearmanRhoSquareMatrixSplit:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplit:
case kStoreCosineSimilaritySquareMatrixSplit:
case kStoreJaccardIndexSquareMatrixSplit:
case kStoreOchiaiSimilaritySquareMatrixSplit:
case kStorePearsonPhiSimilaritySquareMatrixSplit:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplit:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit:
bs_print_sqr_split_store_frequency_to_txt(lookup,
sqr_store,
stdout);
break;
case kStorePearsonRSquareMatrixBzip2:
case kStoreSpearmanRhoSquareMatrixBzip2:
bs_print_sqr_bzip2_store_frequency_to_txt(lookup,
sqr_store,
stdout);
break;
case kStorePearsonRSquareMatrixBzip2Split:
case kStoreSpearmanRhoSquareMatrixBzip2Split:
bs_print_sqr_bzip2_split_store_frequency_to_txt(lookup,
sqr_store,
stdout);
break;
case kStorePearsonRSUT:
case kStoreRandomSUT:
case kStorePearsonRSquareMatrixSplitSingleChunk:
case kStorePearsonRSquareMatrixSplitSingleChunkMetadata:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunk:
case kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk:
case kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunk:
case kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreJaccardIndexSquareMatrixSplitSingleChunk:
case kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk:
case kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk:
case kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk:
case kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk:
case kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata:
case kStoreUndefined:
fprintf(stderr, "Error: You should never see this error! (D)\n");
exit(EXIT_FAILURE);
}
}
else if (bs_globals.store_query_daemon_flag) {
bs_qd_test_dependencies();
fprintf(stderr, "Info: bedextract is located at: [%s]\n", bs_globals.bedextract_path);
fprintf(stderr, "Info: bedops is located at: [%s]\n", bs_globals.bedops_path);
fprintf(stderr, "Info: bedmap is located at: [%s]\n", bs_globals.bedmap_path);
fprintf(stderr, "Info: sort-bed is located at: [%s]\n", bs_globals.sortbed_path);
bs_globals.lookup_ptr = lookup;
bs_globals.sqr_store_ptr = sqr_store;
struct MHD_Daemon *daemon = NULL;
if (!bs_globals.enable_ssl) {
daemon = MHD_start_daemon(MHD_USE_THREAD_PER_CONNECTION,
bs_globals.store_query_daemon_port,
NULL,
NULL,
&bs_qd_answer_to_connection,
NULL,
MHD_OPTION_NOTIFY_COMPLETED, &bs_qd_request_completed,
NULL,
MHD_OPTION_END);
}
else {
daemon = MHD_start_daemon(MHD_USE_THREAD_PER_CONNECTION | MHD_USE_SSL,
bs_globals.store_query_daemon_port,
NULL,
NULL,
&bs_qd_answer_to_connection,
NULL,
MHD_OPTION_HTTPS_MEM_KEY, bs_globals.ssl_key_pem,
MHD_OPTION_HTTPS_MEM_CERT, bs_globals.ssl_cert_pem,
MHD_OPTION_NOTIFY_COMPLETED, &bs_qd_request_completed,
NULL,
MHD_OPTION_END);
}
if (!daemon) {
fprintf(stderr, "Error: Unable to initialize query daemon!\n");
exit(EXIT_FAILURE);
}
fprintf(stdout, "Info: Initialized query httpd...\n");
if (bs_globals.store_query_daemon_hostname) {
fprintf(stdout, "Info: Examples of requests include:\n"\
"\t'$ curl -i -X GET \"%s://%s:%d\"'\n" \
"Or:\n"\
"\t'$ curl -i -X GET \"%s://%s:%d/random?filter-type=greater-than-inclusive&filter-value=0.50\"'\n"\
"Or:\n"\
"\t'$ curl -i -X POST -H \"Content-Type: multipart/form-data\" -F \"file=@test/elements.bed\" \"%s://%s:%d/elements\"'\n"\
"Or:\n"\
"\t'$ curl -i -X POST -H \"Content-Type: multipart/form-data\" -F \"file=@test/elements.bed\" \"%s://%s:%d/elements?filter-type=within-exclusive&filter-value=0.35:1\"'\n"\
"Etc.\n\n"\
"%s",
(bs_globals.enable_ssl ? "https" : "http"),
bs_globals.store_query_daemon_hostname,
bs_globals.store_query_daemon_port,
(bs_globals.enable_ssl ? "https" : "http"),
bs_globals.store_query_daemon_hostname,
bs_globals.store_query_daemon_port,
(bs_globals.enable_ssl ? "https" : "http"),
bs_globals.store_query_daemon_hostname,
bs_globals.store_query_daemon_port,
(bs_globals.enable_ssl ? "https" : "http"),
bs_globals.store_query_daemon_hostname,
bs_globals.store_query_daemon_port,
(bs_globals.enable_ssl ? "(Add the \"-k\" option if using SSL with self-signed certificates.)\n" : ""));
}
else {
fprintf(stdout, "Info: Examples of requests include:\n"\
"\t'$ curl -i -X GET \"%s://hostname:port\"'\n"\
"Or:\n"\
"\t'$ curl -i -X GET \"%s://hostname:port/random?filter-type=greater-than-inclusive&filter-value=0.50\"'\n"\
"Or:\n"\
"\t'$ curl -i -X POST -H \"Content-Type: multipart/form-data\" -F \"file=@test/elements.bed\" \"%s://hostname:port/elements\"'\n"\
"Or:\n"\
"\t'$ curl -i -X POST -H \"Content-Type: multipart/form-data\" -F \"file=@test/elements.bed\" \"%s://hostname:port/elements?filter-type=within-exclusive&filter-value=0.35:1\"'\n"\
"Etc.\n\n"\
"%s",
(bs_globals.enable_ssl ? "https" : "http"),
(bs_globals.enable_ssl ? "https" : "http"),
(bs_globals.enable_ssl ? "https" : "http"),
(bs_globals.enable_ssl ? "https" : "http"),
(bs_globals.enable_ssl ? "(Add the \"-k\" option if using SSL with self-signed certificates.)\n" : ""));
}
fprintf(stdout, "\nPress <Return> to stop the server...\n");
getchar(); /* wait for it... */
fprintf(stdout, "Closing %s daemon...\n", (bs_globals.enable_ssl ? "https" : "http"));
MHD_stop_daemon(daemon);
}
bs_delete_sqr_store(&sqr_store);
break;
case kStoreUndefined:
if (bs_globals.lookup_frequency_flag) {
if (bs_globals.permutation_test_flag) {
bs_permute_lookup(lookup, stdout);
}
else if (!bs_globals.permutation_test_flag) {
bs_print_lookup_frequency(lookup, stdout);
}
}
else {
fprintf(stderr, "Error: You should never see this error! (E)\n");
bs_print_usage(stderr);
exit(EXIT_FAILURE);
}
}
bs_delete_lookup(&lookup);
bs_delete_globals();
return EXIT_SUCCESS;
}
static char*
bs_qd_load_file(const char* fn)
{
FILE* fp = NULL;
char* buf = NULL;
long size = 0;
size = bs_qd_get_file_size(fn);
if (size == 0) {
return NULL;
}
fp = fopen(fn, "rb");
if (!fp) {
return NULL;
}
buf = malloc(size + 1);
if (!buf) {
fclose(fp);
return NULL;