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byte-store.h
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byte-store.h
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#ifndef BYTE_STORE_H_
#define BYTE_STORE_H_
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#ifndef _POSIX_C_SOURCE
#define _POSIX_C_SOURCE 200809L
#endif /* getline() support */
#if __APPLE__
#ifndef HOST_NAME_MAX
#define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
#endif
#endif
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <getopt.h>
#include <inttypes.h>
#include <stdint.h>
#include <time.h>
#include <math.h>
#include <assert.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <sys/socket.h>
#include <sys/time.h>
#include <unistd.h>
#include <float.h>
#include <errno.h>
#include <bzlib.h>
#include <microhttpd.h>
#include <netdb.h>
#include <limits.h>
#include "mt19937.h"
#define BUF_MAX_LEN 4096
#define CHR_MAX_LEN 256
#define COORD_MAX_LEN 20
#define SCORE_MAX_LEN 5
#define DELIMITER_LEN 1
#define OUTPUT_LINE_MAX_LEN (CHR_MAX_LEN * 2) + (COORD_MAX_LEN * 4) + SCORE_MAX_LEN + (DELIMITER_LEN * 6) + 1
#define ID_MAX_LEN 524288
#define FN_MAX_LEN 1024
#define QUERY_MAX_LEN 524288
#define ENTRY_MAX_LEN 20
#define OFFSET_MAX_LEN 20
#define MD_OFFSET_MAX_LEN 20
#define BLOCK_STR_MAX_LEN 13
#define NORMALIZATION_FACTOR_STR_MAX_LEN 13
#define LINE_ID_STR_MAX_LEN 13
#define MULT_IDX_MAX_NUM 4096
#define HOSTNAME_MAX_LEN 8192
#define UPLOAD_FILESIZE_MAX 1048576
#define INITIAL_BUF_CAPACITY 1024
#define PR_SIZET "z"
#define swap(x,y) do \
{ unsigned char swap_temp[sizeof(x) == sizeof(y) ? (signed)sizeof(x) : -1]; \
memcpy(swap_temp,&y,sizeof(x)); \
memcpy(&y,&x, sizeof(x)); \
memcpy(&x,swap_temp,sizeof(x)); \
} while(0)
typedef unsigned char byte_t;
typedef float score_t;
typedef float rank_t;
extern const byte_t kNANEncodedByte;
const byte_t kNANEncodedByte = 0xca;
extern const char* kTestVectorA;
extern const char* kTestVectorB;
extern const char* kTestVectorC;
extern const char* kTestVectorX;
extern const char* kTestVectorY;
extern const char* kTestVectorZ;
extern const char* kTestVectorJ1;
extern const char* kTestVectorJ2;
extern const char* kTestVectorJ3;
extern const char* kTestVectorJz;
extern const char* kTestVectorJu;
extern const char* kTestVectorO1;
extern const char* kTestVectorO2;
extern const char* kTestVectorO3;
extern const char* kTestVectorOz;
extern const char* kTestVectorOu;
extern const char* kTestVectorH1;
extern const char* kTestVectorH2;
extern const char* kTestVectorH3;
extern const char* kTestVectorHz;
extern const char* kTestVectorHu;
extern const char* kTestVectorT1;
extern const char* kTestVectorT2;
extern const char* kTestVectorT3;
extern const char* kTestVectorTz;
extern const char* kTestVectorTu;
extern const char* kTestVectorM1;
extern const char* kTestVectorM2;
extern const char* kTestVectorMz;
extern const char* kTestVectorMu;
const score_t kTestVectorDNormFactor;
const char* kTestVectorD1;
const char* kTestVectorD2;
const char* kTestVectorD3;
const char* kTestVectorDz;
const char* kTestVectorDu;
const char* kTestVectorI1;
const char* kTestVectorI2;
const char* kTestVectorI3;
const char* kTestVectorIz;
const char* kTestVectorIu;
const char* kTestVectorA = "20,8,10,31,50,51,15,41,28,28,11,25,23,21,13,19,14,16,36,38,24,15,35,24,61,31,18,49,19,14,27,19,12,18,15,116,21,28,22,16,11,22,29,31,18,17,9,17,8,14,35,43,10,24,13,19,17,119,33,23,40,10,19,60,12,18,22,7,5,27,40,12,7,21,7,18,6,34,26,6,16,11";
const char* kTestVectorB = "17,10,9,42,57,56,5,49,24,27,14,22,25,16,21,23,22,10,20,29,14,29,34,14,70,33,5,35,11,13,13,20,15,15,55,19,32,26,10,11,12,16,25,22,31,7,8,2,10,9,14,50,9,38,20,21,14,27,31,14,24,15,14,18,16,26,6,3,8,10,58,16,8,19,10,53,4,76,17,14,29,27";
const char* kTestVectorC = "0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0";
const char* kTestVectorX = "1,2,3,20,4";
const char* kTestVectorY = "2,3,1,15,9";
const char* kTestVectorZ = "2,NAN,1,15,9";
const char* kTestVectorJ1 = "0,1,0,0,0,1,1";
const char* kTestVectorJ2 = "0,1,0,1,1,1,1";
const char* kTestVectorJ3 = "0,1,NAN,0,0,0,1";
const char* kTestVectorJz = "0,0,0,0,0,0,0";
const char* kTestVectorJu = "1,1,1,1,1,1,1";
const char* kTestVectorO1 = "0,1,1,0,0,1,1";
const char* kTestVectorO2 = "0,1,0,1,0,0,1";
const char* kTestVectorO3 = "0,1,1,0,1,NAN,0";
const char* kTestVectorOz = "0,0,0,0,0,0,0";
const char* kTestVectorOu = "1,1,1,1,1,1,1";
const char* kTestVectorH1 = "0,1,1,0,0,1,0";
const char* kTestVectorH2 = "1,0,0,1,1,0,1";
const char* kTestVectorH3 = "0,1,0,0,0,0,0";
const char* kTestVectorHz = "0,0,0,0,0,0,0";
const char* kTestVectorHu = "1,1,1,1,1,1,1";
const char* kTestVectorT1 = "0,1,1,0,0,1,1";
const char* kTestVectorT2 = "0,1,0,1,0,0,1";
const char* kTestVectorT3 = "0,1,1,0,1,NAN,0";
const char* kTestVectorTz = "0,0,0,0,0,0,0";
const char* kTestVectorTu = "1,1,1,1,1,1,1";
const char* kTestVectorM1 = "0,1,0,0,0,1,0,1,0,1,0,0";
const char* kTestVectorM2 = "0,1,1,1,1,0,1,0,1,0,1,1";
const char* kTestVectorM3 = "0,1,1,1,1,0,1,0,1,0,NAN,1";
const char* kTestVectorMz = "0,0,0,0,0,0,0,0,0";
const char* kTestVectorMu = "1,1,1,1,1,1,1,1,1";
const score_t kTestVectorDNormFactor = 10.0f;
const char* kTestVectorD1 = "1,5,5,2";
const char* kTestVectorD2 = "3,0,1,1";
const char* kTestVectorD3 = "0,1,1,NAN";
const char* kTestVectorDz = "0,0,0,0";
const char* kTestVectorDu = "5,5,5,5";
const char* kTestVectorI1 = "0.3,0.0,0.6,0.1";
const char* kTestVectorI2 = "0.2,0.1,0.1,0.6";
const char* kTestVectorI3 = "0.0,0.1,0.4,NAN";
const char* kTestVectorIz = "0.0,0.0,0.0,0.0";
const char* kTestVectorIu = "1.0,1.0,1.0,1.0";
extern const score_t kPearsonRTestABCorrelationUnencoded;
extern const score_t kPearsonRTestABCorrelationEncoded;
extern const byte_t kPearsonRTestABCorrelationEncodedByte;
extern const score_t kPearsonRTestACCorrelationUnencoded;
extern const score_t kPearsonRTestACCorrelationEncoded;
extern const byte_t kPearsonRTestACCorrelationEncodedByte;
const score_t kPearsonRTestABCorrelationUnencoded = 0.4134264f;
const score_t kPearsonRTestABCorrelationEncoded = 0.41f;
const byte_t kPearsonRTestABCorrelationEncodedByte = 0x8e;
const score_t kPearsonRTestACCorrelationUnencoded = NAN;
const score_t kPearsonRTestACCorrelationEncoded = NAN;
const byte_t kPearsonRTestACCorrelationEncodedByte = 0xca;
/*
Sanity checks courtesy of R, e.g.:
> x <- c(1,2,3,20,4)
> y <- c(2,3,1,5,4)
> cor(x, y, use="all", method="spearman")
[1] 0.7
etc.
*/
extern const score_t kSpearmanRhoTestXYCorrelationUnencoded;
extern const score_t kSpearmanRhoTestXYCorrelationEncoded;
extern const score_t kSpearmanRhoTestXZCorrelationUnencoded;
extern const score_t kSpearmanRhoTestXZCorrelationEncoded;
extern const byte_t kSpearmanRhoTestXZCorrelationEncodedByte;
extern const score_t kSpearmanRhoTestABCorrelationUnencoded;
extern const score_t kSpearmanRhoTestABCorrelationEncoded;
extern const score_t kSpearmanRhoTestACCorrelationUnencoded;
extern const score_t kSpearmanRhoTestACCorrelationEncoded;
extern const byte_t kSpearmanRhoTestACCorrelationEncodedByte;
const score_t kSpearmanRhoTestXYCorrelationUnencoded = 0.7f;
const score_t kSpearmanRhoTestXYCorrelationEncoded = 0.70f;
const byte_t kSpearmanRhoTestXYCorrelationEncodedByte = 0xab;
const score_t kSpearmanRhoTestABCorrelationUnencoded = 0.6152396f;
const score_t kSpearmanRhoTestABCorrelationEncoded = 0.61f;
const byte_t kSpearmanRhoTestABCorrelationEncodedByte = 0xa2;
const score_t kSpearmanRhoTestXZCorrelationUnencoded = NAN;
const score_t kSpearmanRhoTestXZCorrelationEncoded = NAN;
const byte_t kSpearmanRhoTestXZCorrelationEncodedByte = 0xca;
const score_t kSpearmanRhoTestACCorrelationUnencoded = NAN;
const score_t kSpearmanRhoTestACCorrelationEncoded = NAN;
const byte_t kSpearmanRhoTestACCorrelationEncodedByte = 0xca;
extern const score_t kNormalizedEuclideanDistanceTestD1D2Unencoded;
extern const score_t kNormalizedEuclideanDistanceTestD1D2Encoded;
extern const byte_t kNormalizedEuclideanDistanceTestD1D2EncodedByte;
extern const score_t kNormalizedEuclideanDistanceTestD1D3Unencoded;
extern const score_t kNormalizedEuclideanDistanceTestD1D3Encoded;
extern const byte_t kNormalizedEuclideanDistanceTestD1D3EncodedByte;
extern const score_t kNormalizedEuclideanDistanceTestDzDzUnencoded;
extern const score_t kNormalizedEuclideanDistanceTestDzDzEncoded;
extern const byte_t kNormalizedEuclideanDistanceTestDzDzEncodedByte;
extern const score_t kNormalizedEuclideanDistanceTestDzDuUnencoded;
extern const score_t kNormalizedEuclideanDistanceTestDzDuEncoded;
extern const byte_t kNormalizedEuclideanDistanceTestDzDuEncodedByte;
extern const score_t kNormalizedEuclideanDistanceTestDuDuUnencoded;
extern const score_t kNormalizedEuclideanDistanceTestDuDuEncoded;
extern const byte_t kNormalizedEuclideanDistanceTestDuDuEncodedByte;
const score_t kNormalizedEuclideanDistanceTestD1D2Unencoded = 0.6782330f;
const score_t kNormalizedEuclideanDistanceTestD1D2Encoded = 0.67f;
const byte_t kNormalizedEuclideanDistanceTestD1D2EncodedByte = 0xa8;
const score_t kNormalizedEuclideanDistanceTestD1D3Unencoded = NAN;
const score_t kNormalizedEuclideanDistanceTestD1D3Encoded = NAN;
const byte_t kNormalizedEuclideanDistanceTestD1D3EncodedByte = 0xca;
const score_t kNormalizedEuclideanDistanceTestDzDzUnencoded = 0.0f;
const score_t kNormalizedEuclideanDistanceTestDzDzEncoded = +0.0f;
const byte_t kNormalizedEuclideanDistanceTestDzDzEncodedByte = 0x65;
const score_t kNormalizedEuclideanDistanceTestDzDuUnencoded = 1.0f;
const score_t kNormalizedEuclideanDistanceTestDzDuEncoded = 1.0f;
const byte_t kNormalizedEuclideanDistanceTestDzDuEncodedByte = 0xc9;
const score_t kNormalizedEuclideanDistanceTestDuDuUnencoded = 0.0f;
const score_t kNormalizedEuclideanDistanceTestDuDuEncoded = +0.0f;
const byte_t kNormalizedEuclideanDistanceTestDuDuEncodedByte = 0x65;
extern const score_t kCosineSimilarityTestI1I2Unencoded;
extern const score_t kCosineSimilarityTestI1I2Encoded;
extern const byte_t kCosineSimilarityTestI1I2EncodedByte;
extern const score_t kCosineSimilarityTestI1I3Unencoded;
extern const score_t kCosineSimilarityTestI1I3Encoded;
extern const byte_t kCosineSimilarityTestI1I3EncodedByte;
extern const score_t kCosineSimilarityTestIzIzUnencoded;
extern const score_t kCosineSimilarityTestIzIzEncoded;
extern const byte_t kCosineSimilarityTestIzIzEncodedByte;
extern const score_t kCosineSimilarityTestIzIuUnencoded;
extern const score_t kCosineSimilarityTestIzIuEncoded;
extern const byte_t kCosineSimilarityTestIzIuEncodedByte;
extern const score_t kCosineSimilarityTestIuIuUnencoded;
extern const score_t kCosineSimilarityTestIuIuEncoded;
extern const byte_t kCosineSimilarityTestIuIuEncodedByte;
const score_t kCosineSimilarityTestI1I2Unencoded = 0.4095142f;
const score_t kCosineSimilarityTestI1I2Encoded = 0.40f;
const byte_t kCosineSimilarityTestI1I2EncodedByte = 0x8d;
const score_t kCosineSimilarityTestI1I3Unencoded = NAN;
const score_t kCosineSimilarityTestI1I3Encoded = NAN;
const byte_t kCosineSimilarityTestI1I3EncodedByte = 0xca;
const score_t kCosineSimilarityTestIzIzUnencoded = NAN;
const score_t kCosineSimilarityTestIzIzEncoded = NAN;
const byte_t kCosineSimilarityTestIzIzEncodedByte = 0xca;
const score_t kCosineSimilarityTestIzIuUnencoded = NAN;
const score_t kCosineSimilarityTestIzIuEncoded = NAN;
const byte_t kCosineSimilarityTestIzIuEncodedByte = 0xca;
const score_t kCosineSimilarityTestIuIuUnencoded = 1.0f;
const score_t kCosineSimilarityTestIuIuEncoded = +1.0f;
const byte_t kCosineSimilarityTestIuIuEncodedByte = 0xc9;
extern const score_t kJaccardIndexTestJ1J2Unencoded;
extern const score_t kJaccardIndexTestJ1J2Encoded;
extern const byte_t kJaccardIndexTestJ1J2EncodedByte;
extern const score_t kJaccardIndexTestJ1J3Unencoded;
extern const score_t kJaccardIndexTestJ1J3Encoded;
extern const byte_t kJaccardIndexTestJ1J3EncodedByte;
extern const score_t kJaccardIndexTestJzJzUnencoded;
extern const score_t kJaccardIndexTestJzJzEncoded;
extern const byte_t kJaccardIndexTestJzJzEncodedByte;
extern const score_t kJaccardIndexTestJzJuUnencoded;
extern const score_t kJaccardIndexTestJzJuEncoded;
extern const byte_t kJaccardIndexTestJzJuEncodedByte;
extern const score_t kJaccardIndexTestJuJuUnencoded;
extern const score_t kJaccardIndexTestJuJuEncoded;
extern const byte_t kJaccardIndexTestJuJuEncodedByte;
const score_t kJaccardIndexTestJ1J2Unencoded = 0.6f;
const score_t kJaccardIndexTestJ1J2Encoded = 0.60f;
const byte_t kJaccardIndexTestJ1J2EncodedByte = 0xa1;
const score_t kJaccardIndexTestJ1J3Unencoded = NAN;
const score_t kJaccardIndexTestJ1J3Encoded = NAN;
const byte_t kJaccardIndexTestJ1J3EncodedByte = 0xca;
const score_t kJaccardIndexTestJzJzUnencoded = NAN;
const score_t kJaccardIndexTestJzJzEncoded = NAN;
const byte_t kJaccardIndexTestJzJzEncodedByte = 0xca;
const score_t kJaccardIndexTestJzJuUnencoded = 0.00f;
const score_t kJaccardIndexTestJzJuEncoded = +0.00f;
const byte_t kJaccardIndexTestJzJuEncodedByte = 0x65;
const score_t kJaccardIndexTestJuJuUnencoded = 1.0f;
const score_t kJaccardIndexTestJuJuEncoded = 1.00f;
const byte_t kJaccardIndexTestJuJuEncodedByte = 0xc9;
extern const score_t kOchiaiSimilarityTestO1O2Unencoded;
extern const score_t kOchiaiSimilarityTestO1O2Encoded;
extern const byte_t kOchiaiSimilarityTestO1O2EncodedByte;
extern const score_t kOchiaiSimilarityTestO1O3Unencoded;
extern const score_t kOchiaiSimilarityTestO1O3Encoded;
extern const byte_t kOchiaiSimilarityTestO1O3EncodedByte;
extern const score_t kOchiaiSimilarityTestOzOzUnencoded;
extern const score_t kOchiaiSimilarityTestOzOzEncoded;
extern const byte_t kOchiaiSimilarityTestOzOzEncodedByte;
extern const score_t kOchiaiSimilarityTestOzOuUnencoded;
extern const score_t kOchiaiSimilarityTestOzOuEncoded;
extern const byte_t kOchiaiSimilarityTestOzOuEncodedByte;
extern const score_t kOchiaiSimilarityTestOuOuUnencoded;
extern const score_t kOchiaiSimilarityTestOuOuEncoded;
extern const byte_t kOchiaiSimilarityTestOuOuEncodedByte;
const score_t kOchiaiSimilarityTestO1O2Unencoded = 0.5773503f;
const score_t kOchiaiSimilarityTestO1O2Encoded = 0.57f;
const byte_t kOchiaiSimilarityTestO1O2EncodedByte = 0x9e;
const score_t kOchiaiSimilarityTestO1O3Unencoded = NAN;
const score_t kOchiaiSimilarityTestO1O3Encoded = NAN;
const byte_t kOchiaiSimilarityTestO1O3EncodedByte = 0xca;
const score_t kOchiaiSimilarityTestOzOzUnencoded = 1.0f;
const score_t kOchiaiSimilarityTestOzOzEncoded = 1.00f;
const byte_t kOchiaiSimilarityTestOzOzEncodedByte = 0xc9;
const score_t kOchiaiSimilarityTestOzOuUnencoded = 0.00f;
const score_t kOchiaiSimilarityTestOzOuEncoded = +0.00f;
const byte_t kOchiaiSimilarityTestOzOuEncodedByte = 0x65;
const score_t kOchiaiSimilarityTestOuOuUnencoded = 1.0f;
const score_t kOchiaiSimilarityTestOuOuEncoded = 1.00f;
const byte_t kOchiaiSimilarityTestOuOuEncodedByte = 0xc9;
extern const score_t kPearsonPhiSimilarityTestH1H2Unencoded;
extern const score_t kPearsonPhiSimilarityTestH1H2Encoded;
extern const byte_t kPearsonPhiSimilarityTestH1H2EncodedByte;
extern const score_t kPearsonPhiSimilarityTestH1H3Unencoded;
extern const score_t kPearsonPhiSimilarityTestH1H3Encoded;
extern const byte_t kPearsonPhiSimilarityTestH1H3EncodedByte;
extern const score_t kPearsonPhiSimilarityTestHzHzUnencoded;
extern const score_t kPearsonPhiSimilarityTestHzHzEncoded;
extern const byte_t kPearsonPhiSimilarityTestHzHzEncodedByte;
extern const score_t kPearsonPhiSimilarityTestHzHuUnencoded;
extern const score_t kPearsonPhiSimilarityTestHzHuEncoded;
extern const byte_t kPearsonPhiSimilarityTestHzHuEncodedByte;
extern const score_t kPearsonPhiSimilarityTestHuHuUnencoded;
extern const score_t kPearsonPhiSimilarityTestHuHuEncoded;
extern const byte_t kPearsonPhiSimilarityTestHuHuEncodedByte;
const score_t kPearsonPhiSimilarityTestH1H2Unencoded = -1.0000000f;
const score_t kPearsonPhiSimilarityTestH1H2Encoded = -1.00f;
const byte_t kPearsonPhiSimilarityTestH1H2EncodedByte = 0x00;
const score_t kPearsonPhiSimilarityTestH1H3Unencoded = 0.4714045f;
const score_t kPearsonPhiSimilarityTestH1H3Encoded = 0.47f;
const byte_t kPearsonPhiSimilarityTestH1H3EncodedByte = 0x94;
const score_t kPearsonPhiSimilarityTestHzHzUnencoded = 1.0f;
const score_t kPearsonPhiSimilarityTestHzHzEncoded = 1.00f;
const byte_t kPearsonPhiSimilarityTestHzHzEncodedByte = 0xc9;
const score_t kPearsonPhiSimilarityTestHzHuUnencoded = -1.00f;
const score_t kPearsonPhiSimilarityTestHzHuEncoded = -1.00f;
const byte_t kPearsonPhiSimilarityTestHzHuEncodedByte = 0x00;
const score_t kPearsonPhiSimilarityTestHuHuUnencoded = 1.0f;
const score_t kPearsonPhiSimilarityTestHuHuEncoded = 1.00f;
const byte_t kPearsonPhiSimilarityTestHuHuEncodedByte = 0xc9;
extern const score_t kRogersAndTanimotoSimilarityTestT1T2Unencoded;
extern const score_t kRogersAndTanimotoSimilarityTestT1T2Encoded;
extern const byte_t kRogersAndTanimotoSimilarityTestT1T2EncodedByte;
extern const score_t kRogersAndTanimotoSimilarityTestT1T3Unencoded;
extern const score_t kRogersAndTanimotoSimilarityTestT1T3Encoded;
extern const byte_t kRogersAndTanimotoSimilarityTestT1T3EncodedByte;
extern const score_t kRogersAndTanimotoSimilarityTestTzTzUnencoded;
extern const score_t kRogersAndTanimotoSimilarityTestTzTzEncoded;
extern const byte_t kRogersAndTanimotoSimilarityTestTzTzEncodedByte;
extern const score_t kRogersAndTanimotoSimilarityTestTzTuUnencoded;
extern const score_t kRogersAndTanimotoSimilarityTestTzTuEncoded;
extern const byte_t kRogersAndTanimotoSimilarityTestTzTuEncodedByte;
extern const score_t kRogersAndTanimotoSimilarityTestTuTuUnencoded;
extern const score_t kRogersAndTanimotoSimilarityTestTuTuEncoded;
extern const byte_t kRogersAndTanimotoSimilarityTestTuTuEncodedByte;
const score_t kRogersAndTanimotoSimilarityTestT1T2Unencoded = 0.40f;
const score_t kRogersAndTanimotoSimilarityTestT1T2Encoded = 0.40f;
const byte_t kRogersAndTanimotoSimilarityTestT1T2EncodedByte = 0x8d;
const score_t kRogersAndTanimotoSimilarityTestT1T3Unencoded = NAN;
const score_t kRogersAndTanimotoSimilarityTestT1T3Encoded = NAN;
const byte_t kRogersAndTanimotoSimilarityTestT1T3EncodedByte = 0xca;
const score_t kRogersAndTanimotoSimilarityTestTzTzUnencoded = 1.0f;
const score_t kRogersAndTanimotoSimilarityTestTzTzEncoded = 1.00f;
const byte_t kRogersAndTanimotoSimilarityTestTzTzEncodedByte = 0xc9;
const score_t kRogersAndTanimotoSimilarityTestTzTuUnencoded = 0.0f;
const score_t kRogersAndTanimotoSimilarityTestTzTuEncoded = +0.00f;
const byte_t kRogersAndTanimotoSimilarityTestTzTuEncodedByte = 0x65;
const score_t kRogersAndTanimotoSimilarityTestTuTuUnencoded = 1.0f;
const score_t kRogersAndTanimotoSimilarityTestTuTuEncoded = 1.00f;
const byte_t kRogersAndTanimotoSimilarityTestTuTuEncodedByte = 0xc9;
extern const score_t kNormalizedPointwiseMutualInformationTestM1M2Unencoded;
extern const score_t kNormalizedPointwiseMutualInformationTestM1M2Encoded;
extern const byte_t kNormalizedPointwiseMutualInformationTestM1M2EncodedByte;
extern const score_t kNormalizedPointwiseMutualInformationTestM1M3Unencoded;
extern const score_t kNormalizedPointwiseMutualInformationTestM1M3Encoded;
extern const byte_t kNormalizedPointwiseMutualInformationTestM1M3EncodedByte;
extern const score_t kNormalizedPointwiseMutualInformationTestMzMzUnencoded;
extern const score_t kNormalizedPointwiseMutualInformationTestMzMzEncoded;
extern const byte_t kNormalizedPointwiseMutualInformationTestMzMzEncodedByte;
extern const score_t kNormalizedPointwiseMutualInformationTestMzMuUnencoded;
extern const score_t kNormalizedPointwiseMutualInformationTestMzMuEncoded;
extern const byte_t kNormalizedPointwiseMutualInformationTestMzMuEncodedByte;
extern const score_t kNormalizedPointwiseMutualInformationTestMuMuUnencoded;
extern const score_t kNormalizedPointwiseMutualInformationTestMuMuEncoded;
extern const byte_t kNormalizedPointwiseMutualInformationTestMuMuEncodedByte;
const score_t kNormalizedPointwiseMutualInformationTestM1M2Unencoded = 0.3947147f;
const score_t kNormalizedPointwiseMutualInformationTestM1M2Encoded = 0.39f;
const byte_t kNormalizedPointwiseMutualInformationTestM1M2EncodedByte = 0x8c;
const score_t kNormalizedPointwiseMutualInformationTestM1M3Unencoded = NAN;
const score_t kNormalizedPointwiseMutualInformationTestM1M3Encoded = NAN;
const byte_t kNormalizedPointwiseMutualInformationTestM1M3EncodedByte = 0xca;
const score_t kNormalizedPointwiseMutualInformationTestMzMzUnencoded = 1.0f;
const score_t kNormalizedPointwiseMutualInformationTestMzMzEncoded = 1.0f;
const byte_t kNormalizedPointwiseMutualInformationTestMzMzEncodedByte = 0xc9;
const score_t kNormalizedPointwiseMutualInformationTestMzMuUnencoded = -1.0f;
const score_t kNormalizedPointwiseMutualInformationTestMzMuEncoded = -1.0f;
const byte_t kNormalizedPointwiseMutualInformationTestMzMuEncodedByte = 0x00;
const score_t kNormalizedPointwiseMutualInformationTestMuMuUnencoded = 1.0f;
const score_t kNormalizedPointwiseMutualInformationTestMuMuEncoded = 1.0f;
const byte_t kNormalizedPointwiseMutualInformationTestMuMuEncodedByte = 0xc9;
typedef int boolean_t;
extern const boolean_t kTrue;
extern const boolean_t kFalse;
const boolean_t kTrue = 1;
const boolean_t kFalse = 0;
/* encoding to two decimals of precision specifies needed accuracy */
extern const score_t kEpsilon;
extern const score_t kEpsilonLessStringent;
const score_t kEpsilon = 0.0000001f;
const score_t kEpsilonLessStringent = 0.001f;
extern const score_t kSelfCorrelationScore;
const score_t kSelfCorrelationScore = +1.0f;
extern const score_t kNoCorrelationScore;
const score_t kNoCorrelationScore = +0.0f;
extern const int kQueryIndexDelim;
const int kQueryIndexDelim = (int) '-';
extern const int kQueryRangeBetweenDelim;
const int kQueryRangeBetweenDelim = (int) '-';
extern const int kQueryRangeWithinDelim;
const int kQueryRangeWithinDelim = (int) ':';
extern const int kQueryMultipleIndexDelim;
const int kQueryMultipleIndexDelim = (int) ',';
extern const int kSignalDelim;
const int kSignalDelim = (int) ',';
extern const int kSignalByteAlignment;
const int kSignalByteAlignment = 64;
typedef struct signal {
uint32_t n;
score_t* data;
boolean_t data_contains_nan;
score_t mean;
score_t sd;
rank_t* ranks;
score_t mean_ranks;
score_t sd_ranks;
} signal_t;
typedef struct element {
char* chr;
uint64_t start;
uint64_t stop;
char* id;
signal_t* signal;
} element_t;
typedef struct lookup {
uint64_t capacity;
uint32_t nelems;
element_t** elems;
} lookup_t;
typedef struct store_attr {
uint32_t nelems;
uint64_t nbytes;
char* fn;
} store_attr_t;
typedef struct sut_store {
store_attr_t* attr;
} sut_store_t;
typedef struct sqr_store {
store_attr_t* attr;
} sqr_store_t;
typedef struct store_buf_node {
byte_t data;
struct store_buf_node* next;
} store_buf_node_t;
typedef struct store_buf_row_node {
struct store_buf_node* head;
struct store_buf_node* tail;
} store_buf_row_node_t;
typedef enum store_type {
kStorePearsonRSUT = 0,
kStorePearsonRSquareMatrix,
kStorePearsonRSquareMatrixSplit,
kStorePearsonRSquareMatrixSplitSingleChunk,
kStorePearsonRSquareMatrixSplitSingleChunkMetadata,
kStorePearsonRSquareMatrixBzip2,
kStorePearsonRSquareMatrixBzip2Split,
kStoreSpearmanRhoSquareMatrix,
kStoreSpearmanRhoSquareMatrixSplit,
kStoreSpearmanRhoSquareMatrixSplitSingleChunk,
kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadata,
kStoreSpearmanRhoSquareMatrixBzip2,
kStoreSpearmanRhoSquareMatrixBzip2Split,
kStoreNormalizedEuclideanDistanceSquareMatrix,
kStoreNormalizedEuclideanDistanceSquareMatrixSplit,
kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunk,
kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadata,
kStoreCosineSimilaritySquareMatrix,
kStoreCosineSimilaritySquareMatrixSplit,
kStoreCosineSimilaritySquareMatrixSplitSingleChunk,
kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadata,
kStoreJaccardIndexSquareMatrix,
kStoreJaccardIndexSquareMatrixSplit,
kStoreJaccardIndexSquareMatrixSplitSingleChunk,
kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadata,
kStoreOchiaiSimilaritySquareMatrix,
kStoreOchiaiSimilaritySquareMatrixSplit,
kStoreOchiaiSimilaritySquareMatrixSplitSingleChunk,
kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadata,
kStorePearsonPhiSimilaritySquareMatrix,
kStorePearsonPhiSimilaritySquareMatrixSplit,
kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunk,
kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadata,
kStoreRogersAndTanimotoSimilaritySquareMatrix,
kStoreRogersAndTanimotoSimilaritySquareMatrixSplit,
kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunk,
kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadata,
kStoreNormalizedPointwiseMutualInformationSquareMatrix,
kStoreNormalizedPointwiseMutualInformationSquareMatrixSplit,
kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunk,
kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadata,
kStoreRandomSUT,
kStoreRandomSquareMatrix,
kStoreRandomBufferedSquareMatrix,
kStoreUndefined
} store_type_t;
/* the order here is important, due to the integer value being used in metadata */
typedef enum score_variety {
kScoreVarietyPearsonR = 0,
kScoreVarietySpearmanRho,
kScoreVarietyJaccardIndex,
kScoreVarietyOchiaiSimilarity,
kScoreVarietyPearsonPhiSimilarity,
kScoreVarietyRogersAndTanimotoSimilarity,
kScoreVarietyNormalizedPointwiseMutualInformation,
kScoreVarietyNormalizedEuclideanDistance,
kScoreVarietyCosineSimilarity,
kScoreVarietyUndefined
} score_variety_t;
extern const char* kStorePearsonRSUTStr;
extern const char* kStorePearsonRSquareMatrixStr;
extern const char* kStorePearsonRSquareMatrixSplitStr;
extern const char* kStorePearsonRSquareMatrixSplitSingleChunkStr;
extern const char* kStorePearsonRSquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStorePearsonRSquareMatrixBzip2Str;
extern const char* kStorePearsonRSquareMatrixBzip2SplitStr;
extern const char* kStoreSpearmanRhoSquareMatrixStr;
extern const char* kStoreSpearmanRhoSquareMatrixSplitStr;
extern const char* kStoreSpearmanRhoSquareMatrixSplitSingleChunkStr;
extern const char* kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStoreSpearmanRhoSquareMatrixBzip2Str;
extern const char* kStoreSpearmanRhoSquareMatrixBzip2SplitStr;
extern const char* kStoreNormalizedEuclideanDistanceSquareMatrixStr;
extern const char* kStoreNormalizedEuclideanDistanceSquareMatrixSplitStr;
extern const char* kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkStr;
extern const char* kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStoreCosineSimilaritySquareMatrixStr;
extern const char* kStoreCosineSimilaritySquareMatrixSplitStr;
extern const char* kStoreCosineSimilarityMatrixSplitSingleChunkStr;
extern const char* kStoreCosineSimilaritySplitSingleChunkMetadataStr;
extern const char* kStoreJaccardIndexSquareMatrixStr;
extern const char* kStoreJaccardIndexSquareMatrixSplitStr;
extern const char* kStoreJaccardIndexSquareMatrixSplitSingleChunkStr;
extern const char* kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStoreOchiaiSimilaritySquareMatrixStr;
extern const char* kStoreOchiaiSimilaritySquareMatrixSplitStr;
extern const char* kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkStr;
extern const char* kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStorePearsonPhiSimilaritySquareMatrixStr;
extern const char* kStorePearsonPhiSimilaritySquareMatrixSplitStr;
extern const char* kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkStr;
extern const char* kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStoreRogersAndTanimotoSimilaritySquareMatrixStr;
extern const char* kStoreRogersAndTanimotoSimilaritySquareMatrixSplitStr;
extern const char* kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkStr;
extern const char* kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixStr;
extern const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitStr;
extern const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkStr;
extern const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadataStr;
extern const char* kStoreRandomSUTStr;
extern const char* kStoreRandomSquareMatrixStr;
extern const char* kStoreRandomBufferedSquareMatrixStr;
const char* kStorePearsonRSUTStr = "pearson-r-sut";
const char* kStorePearsonRSquareMatrixStr = "pearson-r-sqr";
const char* kStorePearsonRSquareMatrixSplitStr = "pearson-r-sqr-split";
const char* kStorePearsonRSquareMatrixSplitSingleChunkStr = "pearson-r-sqr-split-single-chunk";
const char* kStorePearsonRSquareMatrixSplitSingleChunkMetadataStr = "pearson-r-sqr-split-single-chunk-metadata";
const char* kStorePearsonRSquareMatrixBzip2Str = "pearson-r-sqr-bzip2";
const char* kStorePearsonRSquareMatrixBzip2SplitStr = "pearson-r-sqr-bzip2-split";
const char* kStoreSpearmanRhoSquareMatrixStr = "spearman-rho-sqr";
const char* kStoreSpearmanRhoSquareMatrixSplitStr = "spearman-rho-sqr-split";
const char* kStoreSpearmanRhoSquareMatrixSplitSingleChunkStr = "spearman-rho-sqr-split-single-chunk";
const char* kStoreSpearmanRhoSquareMatrixSplitSingleChunkMetadataStr = "spearman-rho-sqr-split-single-chunk-metadata";
const char* kStoreSpearmanRhoSquareMatrixBzip2Str = "spearman-rho-sqr-bzip2";
const char* kStoreSpearmanRhoSquareMatrixBzip2SplitStr = "spearman-rho-sqr-bzip2-split";
const char* kStoreNormalizedEuclideanDistanceSquareMatrixStr = "normalized-euclidean-distance-sqr";
const char* kStoreNormalizedEuclideanDistanceSquareMatrixSplitStr = "normalized-euclidean-distance-sqr-split";
const char* kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkStr = "normalized-euclidean-distance-sqr-split-single-chunk";
const char* kStoreNormalizedEuclideanDistanceSquareMatrixSplitSingleChunkMetadataStr = "normalized-euclidean-distance-sqr-split-single-chunk-metadata";
const char* kStoreCosineSimilaritySquareMatrixStr = "cosine-similarity-sqr";
const char* kStoreCosineSimilaritySquareMatrixSplitStr = "cosine-similarity-sqr-split";
const char* kStoreCosineSimilaritySquareMatrixSplitSingleChunkStr = "cosine-similarity-sqr-split-single-chunk";
const char* kStoreCosineSimilaritySquareMatrixSplitSingleChunkMetadataStr = "cosine-similarity-sqr-split-single-chunk-metadata";
const char* kStoreJaccardIndexSquareMatrixStr = "jaccard-index-sqr";
const char* kStoreJaccardIndexSquareMatrixSplitStr = "jaccard-index-sqr-split";
const char* kStoreJaccardIndexSquareMatrixSplitSingleChunkStr = "jaccard-index-sqr-split-single-chunk";
const char* kStoreJaccardIndexSquareMatrixSplitSingleChunkMetadataStr = "jaccard-index-sqr-split-single-chunk-metadata";
const char* kStoreOchiaiSimilaritySquareMatrixStr = "ochiai-similarity-sqr";
const char* kStoreOchiaiSimilaritySquareMatrixSplitStr = "ochiai-similarity-sqr-split";
const char* kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkStr = "ochiai-similarity-sqr-split-single-chunk";
const char* kStoreOchiaiSimilaritySquareMatrixSplitSingleChunkMetadataStr = "ochiai-similarity-sqr-split-single-chunk-metadata";
const char* kStorePearsonPhiSimilaritySquareMatrixStr = "pearson-phi-similarity-sqr";
const char* kStorePearsonPhiSimilaritySquareMatrixSplitStr = "pearson-phi-similarity-sqr-split";
const char* kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkStr = "pearson-phi-similarity-sqr-split-single-chunk";
const char* kStorePearsonPhiSimilaritySquareMatrixSplitSingleChunkMetadataStr = "pearson-phi-similarity-sqr-split-single-chunk-metadata";
const char* kStoreRogersAndTanimotoSimilaritySquareMatrixStr = "rogers-and-tanimoto-similarity-sqr";
const char* kStoreRogersAndTanimotoSimilaritySquareMatrixSplitStr = "rogers-and-tanimoto-similarity-sqr-split";
const char* kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkStr = "rogers-and-tanimoto-similarity-sqr-split-single-chunk";
const char* kStoreRogersAndTanimotoSimilaritySquareMatrixSplitSingleChunkMetadataStr = "rogers-and-tanimoto-similarity-sqr-split-single-chunk-metadata";
const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixStr = "normalized-pointwise-mutual-information-sqr";
const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitStr = "normalized-pointwise-mutual-information-sqr-split";
const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkStr = "normalized-pointwise-mutual-information-sqr-split-single-chunk";
const char* kStoreNormalizedPointwiseMutualInformationSquareMatrixSplitSingleChunkMetadataStr = "normalized-pointwise-mutual-information-sqr-split-single-chunk-metadata";
const char* kStoreRandomSUTStr = "random-sut";
const char* kStoreRandomSquareMatrixStr = "random-sqr";
const char* kStoreRandomBufferedSquareMatrixStr = "random-buffered-sqr";
typedef enum encoding_strategy {
kEncodingStrategyFull = 0,
kEncodingStrategyMidQuarterZero,
kEncodingStrategyCustom,
kEncodingStrategyUndefined
} encoding_strategy_t;
extern const char* kEncodingStrategyFullStr;
extern const char* kEncodingStrategyMidQuarterZeroStr;
extern const char* kEncodingStrategyCustomStr;
extern const score_t kEncodingStrategyDefaultCutoff;
const char* kEncodingStrategyFullStr = "full";
const char* kEncodingStrategyMidQuarterZeroStr = "mid-quarter-zero";
const char* kEncodingStrategyCustomStr = "custom";
const score_t kEncodingStrategyDefaultCutoff = -DBL_MAX;
extern const uint32_t kRowChunkDefaultSize;
extern const uint32_t kRowChunkDefaultOffset;
const uint32_t kRowChunkDefaultSize = UINT32_MAX;
const uint32_t kRowChunkDefaultOffset = UINT32_MAX;
extern const char* kRawMetadataSplitFn;
extern const char* kRawMetadataSplitDirSuffix;
const char* kRawMetadataSplitFn = "blocks.md";
const char* kRawMetadataSplitDirSuffix = ""; /* formerly set to "blocks" -- see kCompressionMetadataSplitDirSuffix */
extern const char* kRawFrequencySuffixFn;
const char* kRawFrequencySuffixFn = "frequency.txt";
extern const uint32_t kCompressionRowChunkMaximumSize;
extern const uint32_t kCompressionBzip2BlockSize100k;
extern const uint32_t kCompressionBzip2BlockSizeFactor;
extern const uint32_t kCompressionBzip2Verbosity;
extern const uint32_t kCompressionBzip2WorkFactor;
extern const uint32_t kCompressionBzip2AbandonPolicy;
extern const uint32_t kCompressionBzip2SmallPolicy;
const uint32_t kCompressionRowChunkMaximumSize = 512;
const uint32_t kCompressionBzip2BlockSize100k = 9;
const uint32_t kCompressionBzip2BlockSizeFactor = 100000;
const uint32_t kCompressionBzip2Verbosity = 0;
const uint32_t kCompressionBzip2WorkFactor = 30;
const uint32_t kCompressionBzip2AbandonPolicy = 0;
const uint32_t kCompressionBzip2SmallPolicy = 0;
extern const char kCompressionMetadataDelimiter;
extern const float kCompressionMetadataVersion;
extern const float kCompressionMetadataVersion1p0;
extern const float kCompressionMetadataVersion1p1;
extern const float kCompressionMetadataVersion1p2;
extern const char* kCompressionMetadataSplitFn;
extern const char* kCompressionMetadataSplitDirSuffix;
const char kCompressionMetadataDelimiter = '|';
const float kCompressionMetadataVersion1p0 = 1.0f;
const float kCompressionMetadataVersion1p1 = 1.1f;
const float kCompressionMetadataVersion1p2 = 1.2f;
const float kCompressionMetadataVersion = 1.2f;
const char* kCompressionMetadataSplitFn = "blocks.md";
const char* kCompressionMetadataSplitDirSuffix = ""; /* formerly set to "blocks" -- this should match kRawMetadataSplitDirSuffix */
extern const uint32_t kPermutationTestDefaultCount;
extern const score_t kPermutationTestDefaultPrecision;
extern const score_t kPermutationTestDefaultAlpha;
extern const uint32_t kPermutationTestDefaultSignificanceLevel;
const uint32_t kPermutationTestDefaultCount = 0;
const score_t kPermutationTestDefaultPrecision = 0.01f;
const score_t kPermutationTestDefaultAlpha = 0.01f;
const uint32_t kPermutationTestDefaultSignificanceLevel = 3;
typedef struct metadata {
score_variety_t score_variety;
off_t* offsets;
size_t count;
size_t block_row_size;
score_t normalization_factor;
double version;
} metadata_t;
extern const uint32_t kQueryIndexDefaultStart;
extern const uint32_t kQueryIndexDefaultEnd;
extern const char* kQueryRangeDefaultChromosome;
extern const uint64_t kQueryRangeDefaultStart;
extern const uint64_t kQueryRangeDefaultEnd;
const uint32_t kQueryIndexDefaultStart = 0;
const uint32_t kQueryIndexDefaultEnd = 0;
const char* kQueryRangeDefaultChromosome = "chrXYZ";
const uint64_t kQueryRangeDefaultStart = 0;
const uint64_t kQueryRangeDefaultEnd = 0;
typedef struct bed {
char* chromosome;
uint64_t start;
uint64_t end;
} bed_t;
typedef enum query_kind {
kQueryKindIndex,
kQueryKindMultipleIndices,
kQueryKindMultipleIndicesFromFile,
kQueryKindMultipleRowAndColumnIndicesFromFile,
kQueryKindRange,
kQueryKindDiagonalOffset,
kQueryKindUndefined
} query_kind_t;
extern const query_kind_t kQueryKindDefaultKind;
const query_kind_t kQueryKindDefaultKind = kQueryKindUndefined;
typedef enum score_filter {
kScoreFilterNone = 0,
kScoreFilterGtEq,
kScoreFilterGt,
kScoreFilterEq,
kScoreFilterLtEq,
kScoreFilterLt,
kScoreFilterRangedWithinExclusive,
kScoreFilterRangedWithinInclusive,
kScoreFilterRangedOutsideExclusive,
kScoreFilterRangedOutsideInclusive,
kScoreFilterUndefined
} score_filter_t;
extern const score_filter_t kScoreDefaultFilter;
const score_filter_t kScoreDefaultFilter = kScoreFilterNone;
extern const char* kScoreFilterGtEqStr;
extern const char* kScoreFilterGtStr;
extern const char* kScoreFilterEqStr;
extern const char* kScoreFilterLtEqStr;
extern const char* kScoreFilterLtStr;
extern const char* kScoreFilterRangedWithinExclusiveStr;
extern const char* kScoreFilterRangedWithinInclusiveStr;
extern const char* kScoreFilterRangedOutsideExclusiveStr;
extern const char* kScoreFilterRangedOutsideInclusiveStr;
const char* kScoreFilterGtEqStr = "greater-than-inclusive";
const char* kScoreFilterGtStr = "greater-than-exclusive";
const char* kScoreFilterEqStr = "equal";
const char* kScoreFilterLtEqStr = "less-than-inclusive";
const char* kScoreFilterLtStr = "less-than-exclusive";
const char* kScoreFilterRangedWithinExclusiveStr = "within-exclusive";
const char* kScoreFilterRangedWithinInclusiveStr = "within-inclusive";
const char* kScoreFilterRangedOutsideExclusiveStr = "outside-exclusive";
const char* kScoreFilterRangedOutsideInclusiveStr = "outside-inclusive";
typedef enum diagonal_side {
kDiagonalSideLowerTriangle = 0,
kDiagonalSideUpperTriangle,
kDiagonalSideUndefined
} diagonal_side_t;
static struct bs_globals_t {
boolean_t store_create_flag;
boolean_t store_query_flag;
boolean_t store_query_daemon_flag;
int32_t store_query_daemon_port;
char* store_query_daemon_hostname;
boolean_t store_frequency_flag;
query_kind_t store_query_kind;
char store_query_str[QUERY_MAX_LEN];
size_t store_query_idx_start;
size_t store_query_idx_end;
size_t* store_query_indices;
uint32_t store_query_indices_num;
uint32_t store_query_indices_capacity;
size_t* store_query_indices_starts;
size_t* store_query_indices_ends;
bed_t* store_query_range_start;
bed_t* store_query_range_end;
score_filter_t store_filter;
score_t score_filter_cutoff;
score_t score_filter_cutoff_lower_bound;
score_t score_filter_cutoff_upper_bound; /* for threshold ranges */
boolean_t score_filter_range_set;
boolean_t store_filter_mutual_set;
boolean_t rng_seed_flag;
uint32_t rng_seed_value;
char lookup_fn[FN_MAX_LEN];
char store_fn[FN_MAX_LEN];
char store_type_str[BUF_MAX_LEN];
store_type_t store_type;
encoding_strategy_t encoding_strategy;
char encoding_strategy_str[BUF_MAX_LEN];
score_t encoding_cutoff_zero_min;
score_t encoding_cutoff_zero_max;
uint32_t store_row_chunk_size;
uint32_t store_row_chunk_offset;
boolean_t store_chunk_size_specified_flag;
boolean_t store_single_chunk_flag;
boolean_t store_compression_flag;
boolean_t lookup_frequency_flag;
boolean_t permutation_test_flag;
uint32_t permutation_count;
score_t permutation_precision;
score_t permutation_alpha;
uint32_t permutation_significance_level;
boolean_t zero_sd_warning_issued;
score_t* score_ptr;
lookup_t* lookup_ptr;
sqr_store_t* sqr_store_ptr;
char* bedextract_path;
char* bedops_path;
char* bedmap_path;
char* sortbed_path;
boolean_t enable_ssl;
char* ssl_key_pem;
char* ssl_cert_pem;
uint32_t diagonal_offset_value;
diagonal_side_t diagonal_offset_side;
boolean_t score_normalization_factor_specified_flag;
score_t score_normalization_factor;
} bs_globals;
static struct option bs_client_long_options[] = {
{ "store-type", required_argument, NULL, 't' },
{ "store-create", no_argument, NULL, 'c' },
{ "store-query", no_argument, NULL, 'q' },
{ "store-query-daemon", required_argument, NULL, 'Q' },
{ "store-frequency", no_argument, NULL, 'f' },
{ "store-row-chunk-size", required_argument, NULL, 'r' },
{ "store-row-chunk-offset", required_argument, NULL, 'k' },
{ "score-filter-gteq", required_argument, NULL, '2' },
{ "score-filter-gt", required_argument, NULL, '3' },
{ "score-filter-eq", required_argument, NULL, '4' },
{ "score-filter-lteq", required_argument, NULL, '5' },
{ "score-filter-lt", required_argument, NULL, '6' },
{ "score-filter-ranged-within-exclusive", required_argument, NULL, '7' },
{ "score-filter-ranged-within-inclusive", required_argument, NULL, '8' },
{ "score-filter-ranged-outside-exclusive", required_argument, NULL, '9' },
{ "score-filter-ranged-outside-inclusive", required_argument, NULL, '0' },
{ "score-normalization-factor", required_argument, NULL, 'F' },
{ "mutual-query", no_argument, NULL, 'm' },
{ "index-query", required_argument, NULL, 'i' },
{ "multiple-index-query", required_argument, NULL, 'w' },
{ "multiple-index-query-from-file", required_argument, NULL, 'z' },
{ "multiple-row-and-column-index-query-from-file", required_argument, NULL, 'Z' },
{ "range-query", required_argument, NULL, 'g' },
{ "diagonal-offset-query", required_argument, NULL, 'b' },
{ "lookup", required_argument, NULL, 'l' },
{ "store", required_argument, NULL, 's' },
{ "encoding-strategy", required_argument, NULL, 'e' },
{ "encoding-cutoff-zero-min", required_argument, NULL, 'n' },
{ "encoding-cutoff-zero-max", required_argument, NULL, 'x' },
{ "lookup-frequency", no_argument, NULL, 'u' },
{ "permutation-test", no_argument, NULL, 'y' },
{ "permutation-count", required_argument, NULL, 'o' },
{ "permutation-precision", required_argument, NULL, 'p' },
{ "permutation-alpha", required_argument, NULL, 'a' },
{ "permutation-significance-level", required_argument, NULL, 'v' },
{ "rng-seed", required_argument, NULL, 'd' },
{ "enable-ssl", no_argument, NULL, 'E' },
{ "ssl-key", required_argument, NULL, 'K' },
{ "ssl-cert", required_argument, NULL, 'C' },
{ "test-pearson-r", no_argument, NULL, 'P' },
{ "test-spearman-rho", no_argument, NULL, 'S' },
{ "test-normalized-euclidean-distance", no_argument, NULL, 'D' },
{ "test-cosine-similarity", no_argument, NULL, 'I' },
{ "test-jaccard-index", no_argument, NULL, 'J' },
{ "test-ochiai-similarity", no_argument, NULL, 'O' },
{ "test-pearson-phi-similarity", no_argument, NULL, 'H' },
{ "test-rogers-and-tanimoto-similarity", no_argument, NULL, 'T' },
{ "test-normalized-pointwise-mutual-information", no_argument, NULL, 'M' },
{ "test-score-encoder", no_argument, NULL, 'N' },
{ "help", no_argument, NULL, 'h' },
{ NULL, no_argument, NULL, 0 }
};
static const char* bs_client_opt_string = "t:cqQ:fr:k:2:3:4:5:6:7:8:9:0:F:mi:w:z:Z:g:b:l:s:e:n:x:uyo:p:a:v:d:EK:C:SDIPJOHTMNh?";
static const char* bs_name = "byte-store";
/**
* @brief bs_encode_byte_to_score_table[]
*
* @details Converts encoded byte to assigned bin interval start,
* e.g., 0x64 maps to -0.00 or (-0.01, -0.00], while
* 0x65 maps to +0.00 or [+0.00, +0.01).
*
* Note the two bins for -0.00 and +0.00. This allows
* mapping of scores between -0.01, 0.00, and 0.01 to
* be mapped to two seperate bytes.
*
* Bins are arranged in base-16 for convenience: read from
* left to right to get bytes 0xI0 through 0xIf; read down
* from top to bottom to get bytes 0x0J through 0xfJ.
*/
static const score_t bs_encode_byte_to_score_table[256] =
{-1.00, -0.99, -0.98, -0.97, -0.96, -0.95, -0.94, -0.93, -0.92, -0.91, -0.90, -0.89, -0.88, -0.87, -0.86, -0.85,
-0.84, -0.83, -0.82, -0.81, -0.80, -0.79, -0.78, -0.77, -0.76, -0.75, -0.74, -0.73, -0.72, -0.71, -0.70, -0.69,
-0.68, -0.67, -0.66, -0.65, -0.64, -0.63, -0.62, -0.61, -0.60, -0.59, -0.58, -0.57, -0.56, -0.55, -0.54, -0.53,
-0.52, -0.51, -0.50, -0.49, -0.48, -0.47, -0.46, -0.45, -0.44, -0.43, -0.42, -0.41, -0.40, -0.39, -0.38, -0.37,
-0.36, -0.35, -0.34, -0.33, -0.32, -0.31, -0.30, -0.29, -0.28, -0.27, -0.26, -0.25, -0.24, -0.23, -0.22, -0.21,
-0.20, -0.19, -0.18, -0.17, -0.16, -0.15, -0.14, -0.13, -0.12, -0.11, -0.10, -0.09, -0.08, -0.07, -0.06, -0.05,
-0.04, -0.03, -0.02, -0.01, -0.00, +0.00, +0.01, +0.02, +0.03, +0.04, +0.05, +0.06, +0.07, +0.08, +0.09, +0.10,
+0.11, +0.12, +0.13, +0.14, +0.15, +0.16, +0.17, +0.18, +0.19, +0.20, +0.21, +0.22, +0.23, +0.24, +0.25, +0.26,
+0.27, +0.28, +0.29, +0.30, +0.31, +0.32, +0.33, +0.34, +0.35, +0.36, +0.37, +0.38, +0.39, +0.40, +0.41, +0.42,
+0.43, +0.44, +0.45, +0.46, +0.47, +0.48, +0.49, +0.50, +0.51, +0.52, +0.53, +0.54, +0.55, +0.56, +0.57, +0.58,
+0.59, +0.60, +0.61, +0.62, +0.63, +0.64, +0.65, +0.66, +0.67, +0.68, +0.69, +0.70, +0.71, +0.72, +0.73, +0.74,
+0.75, +0.76, +0.77, +0.78, +0.79, +0.80, +0.81, +0.82, +0.83, +0.84, +0.85, +0.86, +0.87, +0.88, +0.89, +0.90,
+0.91, +0.92, +0.93, +0.94, +0.95, +0.96, +0.97, +0.98, +0.99, +1.00, NAN, +0.00, +0.00, +0.00, +0.00, +0.00,
+0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00,
+0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00,
+0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00};
/**
* @brief bs_encode_unsigned_char_to_score_mqz_table[]
*
* @details Converts encoded byte to assigned bin interval start,
* but maps (-0.25, +0.25) to +0.00
*/
static const score_t bs_encode_byte_to_score_mqz_table[256] =
{-1.00, -0.99, -0.98, -0.97, -0.96, -0.95, -0.94, -0.93, -0.92, -0.91, -0.90, -0.89, -0.88, -0.87, -0.86, -0.85,
-0.84, -0.83, -0.82, -0.81, -0.80, -0.79, -0.78, -0.77, -0.76, -0.75, -0.74, -0.73, -0.72, -0.71, -0.70, -0.69,
-0.68, -0.67, -0.66, -0.65, -0.64, -0.63, -0.62, -0.61, -0.60, -0.59, -0.58, -0.57, -0.56, -0.55, -0.54, -0.53,
-0.52, -0.51, -0.50, -0.49, -0.48, -0.47, -0.46, -0.45, -0.44, -0.43, -0.42, -0.41, -0.40, -0.39, -0.38, -0.37,
-0.36, -0.35, -0.34, -0.33, -0.32, -0.31, -0.30, -0.29, -0.28, -0.27, -0.26, -0.25, +0.00, +0.00, +0.00, +0.00,
+0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00,
+0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00,
+0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.00, +0.25, +0.26,
+0.27, +0.28, +0.29, +0.30, +0.31, +0.32, +0.33, +0.34, +0.35, +0.36, +0.37, +0.38, +0.39, +0.40, +0.41, +0.42,