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1. Changed logger.info to logger.warn in PairHMMLikelihoodCalculationEngine.java 

2. Committing the right set of files after rebase
This commit is contained in:
Karthik Gururaj 2014-02-28 16:08:28 -08:00
parent 37526dfad5
commit 1b395a871a
11 changed files with 165 additions and 61 deletions
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2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -98,7 +98,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
}
catch(UnsatisfiedLinkError ule)
{
logger.info("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING");
logger.warn("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING");
return new LoglessPairHMM();
}
case DEBUG_VECTOR_LOGLESS_CACHING:

16
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java
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@ -449,21 +449,7 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
})
@Ensures("constantsAreInitialized")
protected static void initializeProbabilities(final double[][] transition, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
for (int i = 0; i < insertionGOP.length; i++) {
final int qualIndexGOP = Math.min(insertionGOP[i] + deletionGOP[i], Byte.MAX_VALUE);
transition[i+1][matchToMatch] = QualityUtils.qualToProb((byte) qualIndexGOP);
transition[i+1][indelToMatch] = QualityUtils.qualToProb(overallGCP[i]);
transition[i+1][matchToInsertion] = QualityUtils.qualToErrorProb(insertionGOP[i]);
transition[i+1][insertionToInsertion] = QualityUtils.qualToErrorProb(overallGCP[i]);
transition[i+1][matchToDeletion] = QualityUtils.qualToErrorProb(deletionGOP[i]);
transition[i+1][deletionToDeletion] = QualityUtils.qualToErrorProb(overallGCP[i]);
//TODO it seems that it is not always the case that matchToMatch + matchToDeletion + matchToInsertion == 1.
//TODO We have detected cases of 1.00002 which can cause problems downstream. This are typically masked
//TODO by the fact that we always add a indelToMatch penalty to all PairHMM likelihoods (~ -0.1)
//TODO This is in fact not well justified and although it does not have any effect (since is equally added to all
//TODO haplotypes likelihoods) perhaps we should just remove it eventually and fix this != 1.0 issue here.
}
PairHMMModel.qualToTransProbs(transition,insertionGOP,deletionGOP,overallGCP);
}
/**

5
public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc
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@ -14,7 +14,6 @@ char* LoadTimeInitializerStatsNames[] =
"dummy"
};
LoadTimeInitializer g_load_time_initializer;
LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loaded
@ -54,6 +53,10 @@ LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loa
initialize_function_pointers();
//Initialize static members of class
Context<float>::initializeStaticMembers();
Context<double>::initializeStaticMembers();
cout.flush();
}

5
public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
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@ -22,7 +22,10 @@ class LoadTimeInitializer
{
public:
LoadTimeInitializer(); //will be called when library is loaded
~LoadTimeInitializer() { delete m_buffer; }
~LoadTimeInitializer()
{
delete m_buffer;
}
void print_profiling();
void debug_dump(std::string filename, std::string s, bool to_append, bool add_newline=true);
void debug_close();

2
public/VectorPairHMM/src/main/c++/Makefile
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@ -4,7 +4,7 @@
#CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
#CFLAGS=-O2 -W -Wall -march=corei7 -mfpmath=sse -msse4.2 -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
JRE_HOME?=/opt/jdk1.7.0_25/
JRE_HOME?=/opt/jdk1.7.0_25/jre
JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JRE_HOME}/../include -I${JRE_HOME}/../include/linux
COMMON_COMPILATION_FLAGS=$(JNI_COMPILATION_FLAGS) -O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas

5
public/VectorPairHMM/src/main/c++/baseline.cc
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@ -2,8 +2,8 @@
#include "template.h"
#include "utils.h"
#include "LoadTimeInitializer.h"
using namespace std;
template<class NUMBER>
NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
{
@ -62,7 +62,8 @@ NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
int _i = tc->i[r-1] & 127;
int _d = tc->d[r-1] & 127;
int _c = tc->c[r-1] & 127;
p[r][MM] = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
//p[r][MM] = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
SET_MATCH_TO_MATCH_PROB(p[r][MM], _i, _d);
p[r][GapM] = ctx._(1.0) - ctx.ph2pr[_c];
p[r][MX] = ctx.ph2pr[_i];
p[r][XX] = ctx.ph2pr[_c];

3
public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc
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@ -116,7 +116,8 @@ template<class NUMBER> void CONCAT(CONCAT(initializeVectors,SIMD_ENGINE), PRECIS
int _d = tc->d[r-1] & 127;
int _c = tc->c[r-1] & 127;
*(ptr_p_MM+r-1) = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
//*(ptr_p_MM+r-1) = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
SET_MATCH_TO_MATCH_PROB(*(ptr_p_MM+r-1), _i, _d);
*(ptr_p_GAPM+r-1) = ctx._(1.0) - ctx.ph2pr[_c];
*(ptr_p_MX+r-1) = ctx.ph2pr[_i];
*(ptr_p_XX+r-1) = ctx.ph2pr[_c];

4
public/VectorPairHMM/src/main/c++/run.sh
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@ -8,8 +8,8 @@ then
fi
#-Djava.library.path is needed if you wish to override the default 'packed' library
#java -Djava.library.path=${GSA_ROOT_DIR}/public/VectorPairHMM/src/main/c++ -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar -T HaplotypeCaller \
java -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar -T HaplotypeCaller \
#java -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar -T HaplotypeCaller \
java -Djava.library.path=${GSA_ROOT_DIR}/public/VectorPairHMM/src/main/c++ -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar -T HaplotypeCaller \
--dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
-R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \
-I /data/simulated/sim1M_pairs_final.bam \

173
public/VectorPairHMM/src/main/c++/template.h
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@ -94,57 +94,158 @@ typedef union ALIGNED
ALIGNED double ALIGNED f;
} ALIGNED IF_64 ALIGNED;
template<class T>
struct Context{};
#define MAX_QUAL 254
#define MAX_JACOBIAN_TOLERANCE 8.0
#define JACOBIAN_LOG_TABLE_STEP 0.0001
#define JACOBIAN_LOG_TABLE_INV_STEP (1.0 / JACOBIAN_LOG_TABLE_STEP)
#define MAXN 70000
#define LOG10_CACHE_SIZE (4*MAXN) // we need to be able to go up to 2*(2N) when calculating some of the coefficients
#define JACOBIAN_LOG_TABLE_SIZE ((int) (MAX_JACOBIAN_TOLERANCE / JACOBIAN_LOG_TABLE_STEP) + 1)
template<class NUMBER>
struct ContextBase
{
public:
NUMBER ph2pr[128];
NUMBER INITIAL_CONSTANT;
NUMBER LOG10_INITIAL_CONSTANT;
NUMBER RESULT_THRESHOLD;
static bool staticMembersInitializedFlag;
static NUMBER jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
static NUMBER matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
static void initializeStaticMembers()
{
if(!staticMembersInitializedFlag)
{
//Order of calls important - Jacobian first, then MatchToMatch
initializeJacobianLogTable();
initializeMatchToMatchProb();
staticMembersInitializedFlag = true;
}
}
static void deleteStaticMembers()
{
if(staticMembersInitializedFlag)
{
staticMembersInitializedFlag = false;
}
}
//Called only once during library load - don't bother to optimize with single precision fp
static void initializeJacobianLogTable()
{
for (int k = 0; k < JACOBIAN_LOG_TABLE_SIZE; k++) {
jacobianLogTable[k] = (NUMBER)(log10(1.0 + pow(10.0, -((double) k) * JACOBIAN_LOG_TABLE_STEP)));
}
}
//Called only once per library load - don't bother optimizing with single fp
static void initializeMatchToMatchProb()
{
double LN10 = log(10);
double INV_LN10 = 1.0/LN10;
for (int i = 0, offset = 0; i <= MAX_QUAL; offset += ++i)
for (int j = 0; j <= i; j++) {
double log10Sum = approximateLog10SumLog10(-0.1*i, -0.1*j);
double matchToMatchLog10 =
log1p(-std::min(1.0,pow(10,log10Sum))) * INV_LN10;
matchToMatchProb[offset + j] = (NUMBER)(pow(10,matchToMatchLog10));
}
}
//Called during computation - use single precision where possible
static int fastRound(NUMBER d) {
return (d > ((NUMBER)0.0)) ? (int) (d + ((NUMBER)0.5)) : (int) (d - ((NUMBER)0.5));
}
//Called during computation - use single precision where possible
static NUMBER approximateLog10SumLog10(NUMBER small, NUMBER big) {
// make sure small is really the smaller value
if (small > big) {
NUMBER t = big;
big = small;
small = t;
}
if (isinf(small) == -1 || isinf(big) == -1)
return big;
NUMBER diff = big - small;
if (diff >= ((NUMBER)MAX_JACOBIAN_TOLERANCE))
return big;
// OK, so |y-x| < tol: we use the following identity then:
// we need to compute log10(10^x + 10^y)
// By Jacobian logarithm identity, this is equal to
// max(x,y) + log10(1+10^-abs(x-y))
// we compute the second term as a table lookup with integer quantization
// we have pre-stored correction for 0,0.1,0.2,... 10.0
int ind = fastRound((NUMBER)(diff * ((NUMBER)JACOBIAN_LOG_TABLE_INV_STEP))); // hard rounding
return big + jacobianLogTable[ind];
}
};
template<class NUMBER>
struct Context : public ContextBase<NUMBER>
{};
template<>
struct Context<double>
struct Context<double> : public ContextBase<double>
{
Context()
{
for (int x = 0; x < 128; x++)
ph2pr[x] = pow(10.0, -((double)x) / 10.0);
Context():ContextBase<double>()
{
for (int x = 0; x < 128; x++)
ph2pr[x] = pow(10.0, -((double)x) / 10.0);
INITIAL_CONSTANT = ldexp(1.0, 1020.0);
LOG10_INITIAL_CONSTANT = log10(INITIAL_CONSTANT);
RESULT_THRESHOLD = 0.0;
}
INITIAL_CONSTANT = ldexp(1.0, 1020.0);
LOG10_INITIAL_CONSTANT = log10(INITIAL_CONSTANT);
RESULT_THRESHOLD = 0.0;
}
double LOG10(double v){ return log10(v); }
double LOG10(double v){ return log10(v); }
inline double POW(double b, double e) { return pow(b,e); }
static double _(double n){ return n; }
static double _(float n){ return ((double) n); }
double ph2pr[128];
double INITIAL_CONSTANT;
double LOG10_INITIAL_CONSTANT;
double RESULT_THRESHOLD;
static double _(double n){ return n; }
static double _(float n){ return ((double) n); }
};
template<>
struct Context<float>
struct Context<float> : public ContextBase<float>
{
Context()
{
for (int x = 0; x < 128; x++)
{
ph2pr[x] = powf(10.f, -((float)x) / 10.f);
}
Context() : ContextBase<float>()
{
for (int x = 0; x < 128; x++)
{
ph2pr[x] = powf(10.f, -((float)x) / 10.f);
}
INITIAL_CONSTANT = ldexpf(1.f, 120.f);
LOG10_INITIAL_CONSTANT = log10f(INITIAL_CONSTANT);
RESULT_THRESHOLD = ldexpf(1.f, -110.f);
}
INITIAL_CONSTANT = ldexpf(1.f, 120.f);
LOG10_INITIAL_CONSTANT = log10f(INITIAL_CONSTANT);
RESULT_THRESHOLD = ldexpf(1.f, -110.f);
}
float LOG10(float v){ return log10f(v); }
float LOG10(float v){ return log10f(v); }
inline float POW(float b, float e) { return powf(b,e); }
static float _(double n){ return ((float) n); }
static float _(float n){ return n; }
float ph2pr[128];
float INITIAL_CONSTANT;
float LOG10_INITIAL_CONSTANT;
float RESULT_THRESHOLD;
static float _(double n){ return ((float) n); }
static float _(float n){ return n; }
};
#define SET_MATCH_TO_MATCH_PROB(output, insQual, delQual) \
{ \
int minQual = delQual; \
int maxQual = insQual; \
if (insQual <= delQual) \
{ \
minQual = insQual; \
maxQual = delQual; \
} \
(output) = (MAX_QUAL < maxQual) ? \
((NUMBER)1.0) - ctx.POW(((NUMBER)10), ctx.approximateLog10SumLog10(((NUMBER)-0.1)*minQual, ((NUMBER)-0.1)*maxQual)) \
: ctx.matchToMatchProb[((maxQual * (maxQual + 1)) >> 1) + minQual]; \
}
typedef struct
{

11
public/VectorPairHMM/src/main/c++/utils.cc
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@ -3,12 +3,21 @@
#include "utils.h"
#include "vector_defs.h"
#include "LoadTimeInitializer.h"
using namespace std;
//static members from ConvertChar
uint8_t ConvertChar::conversionTable[255];
//Global function pointers in utils.h
float (*g_compute_full_prob_float)(testcase *tc, float* before_last_log) = 0;
double (*g_compute_full_prob_double)(testcase *tc, double* before_last_log) = 0;
//Static members in ContextBase
bool ContextBase<double>::staticMembersInitializedFlag = false;
double ContextBase<double>::jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
double ContextBase<double>::matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
bool ContextBase<float>::staticMembersInitializedFlag = false;
float ContextBase<float>::jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
float ContextBase<float>::matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
using namespace std;
bool is_avx_supported()
{

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public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so
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