SweeD.h~

-/*  
- *  SweeD
- *
- *  Copyright September 2012 by Nikolaos Alachiotis and Pavlos Pavlidis
- *
- *  This program is free software; you may redistribute it and/or modify its
- *  under the terms of the GNU General Public License as published by the Free
- *  Software Foundation; either version 2 of the License, or (at your option)
- *  any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
- *  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- *  for more details.
- *
- *  For any other enquiries send an email to
- *  Pavlos Pavlidis (pavlidisp@gmail.com) or
- *  Nikolaos Alachiotis (n.alachiotis@gmail.com)
- *  
- */
-
-
-#ifndef _SweeD_H
-#define _SweeD_H
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
-#include <math.h>
-#include <time.h>
-#include <sys/time.h>
-#include <limits.h>
-
-
-#include "SweeD_BFGS.h"
-
-#ifdef _USE_PTHREADS
-#include <pthread.h>
-#include <unistd.h>
-
-#define EXIT 127
-#define BUSYWAIT 0
-#define LIKSFS 1
-#define COMPRVLUT 2
-#define COMPALPHA 3
-
-#endif
-
-#ifdef _DO_CHECKPOINTS
-#include "dmtcpaware.h"
-#endif
-
-#ifdef _ANALYTICAL_SFS
-#include <mpfr.h>
-#include <float.h>
-#define ACC 10000
-#define APPROX 0
-#define TOLTIME 1e-7
-#define RESCALE 1
-#endif
-
-#define ENTRIES_PER_INT 32
-#define DENOMINATOR_OFFSET 0.00001
-#define REGISTER_WIDTH 32
-#define MAXSIZE 10000
-#define INFILENAMESIZE 1000
-#define SEQNAMESIZE 1000
-#define DECREASE 0.99
-#define MINSNPPERWINDOW 5
-#define STRINGLENGTH 100
-#define VCF_HLENGTH 9 // number of fields in the VCF header line
-#define MAX_CHROM_NAME_VCF 100
-#define MAX_STATES_VCF 5
-
-#define RESULTS_DEFAULT 0
-#define RESULTS_ALL 1
-
-#define RSQUARE 0
-#define DOM 1
-#define ABSDOM 2
-#define JUSTD 3
-#define ABSD 4
-#define ABSDOM2 5
-
-#define ZERO '0'
-#define ONE  '1'
-#define GAP '-'
-#define AD 'A'
-#define CY 'C'
-#define GU 'G'
-#define TH 'T'
-#define UN 'N'
-
-#define BINARY 2
-#define BINARY_WITH_GAPS 3
-#define DNA 4
-#define DNA_WITH_GAPS 5
-#define STATESALL 8
-
-#define OTHER_FORMAT -1
-#define MS_FORMAT 0
-#define FASTA_FORMAT 1
-#define MACS_FORMAT 2
-#define VCF_FORMAT 3
-#define SF_FORMAT 4
-
-#define INTOKS 8
-
-#define N_REF 2
-#define N_ALT 3
-#define N_INFO 6
-#define MAX_STATES 100
-#define MAXINT 2147483647
-
-
-char bits_in_16bits [0x1u << 16];
-
-int linkage_disequilibrium;
-
-int borderTol;
-
-int VCF_header_lines;
-char VCF_alignment_name [MAX_CHROM_NAME_VCF];
-int VCF_first_SNP;
-int nxtVCFalignment;
-
-char runName[INFILENAMESIZE];
-
-typedef float cor_t;
-
-
-
-cor_t ABS (cor_t input);
-
-double mainTime0;
-
-int map[INTOKS];
-
-int nofTokens;
-
-int nofSamples;
-
-typedef int al_t;
-typedef double t_sfs;
-
-struct pattern
-{
-	int x;
-	int n;
-	unsigned char f;
-	int c;
-	struct pattern * nxt;		
-};
-
-typedef struct 
-{
- 	al_t	*n; // number of valid bases in every site
-	al_t	*n_t; // number of valid bases in every site
-	al_t *x; // number of derived bases in every site
-	al_t *x_t; // number of derived bases in every site
-	float 	       * positions;
-	int 	       * positionsInd;
-	int 	       * p_t;
-	unsigned char *folded;
-	unsigned char *f_t;
-	unsigned char userSetFolded;
-	unsigned char userSFS;
-	char* outgroupSequence;
-  	char* outgroupName;
-	int outgroupIndex;
-	int sequences;
-  	int foldedFormat; // if outgroup exists we set this to zero
-	int 		 segsites;	
-	int		 length;
-
-	int minn;
-	int minx;	
-  	int maxn;
-	int maxx;
-
-	al_t * stateA;
-	al_t * stateC;
-	al_t * stateG;
-	al_t * stateT;
-
-
-	t_sfs * SFS;
-	t_sfs * tmpSFS;
-	int startSFS;
-	int endSFS;
-
-	int * ng;
-
-	t_sfs * lb;
-	t_sfs * ub;
-
-	int params;
-
-	al_t * n_pat;
-	al_t * x_pat;
-	unsigned char * f_pat;
-	int *  c_pat;
-	int patterns;
-
-	t_sfs *** gridProbs;
-	t_sfs * gridADs;
-	t_sfs interval;
-	t_sfs logAD0;	
-
-	t_sfs * baseLikelihood;
-
-	struct pattern * patternList;
-	
-	float sweepStep;
-
-	int discSites;
-
-#ifdef _USE_PTHREADS
-	t_sfs * threadScoresLIKSFS;
-#endif
-
-} alignment_struct;
-
-alignment_struct * alignment;
-
-double * rv;
-double ** rvLUT;
-double ** rvLUT2;
-
-
-#define GRIDSIZE 300
-#define LOCALGRIDSIZE 100
-
-double div6; 
-
-
-typedef struct
-{
-	double * val;
-	int * sc;
-
-} factorial_LUT;
-
-factorial_LUT * factLUT;
-
-
-typedef struct
-{
-
-  int 		sfRealPos; 
-  t_sfs		likelihood; 
-  t_sfs		alpha; 
- 
-} clr_struct;
-
-clr_struct * clr;
-
-#ifdef _ANALYTICAL_SFS
-typedef struct
-{
-	double t;
-	double d;
-} event;
-
-int eventsTotal;
-event * eventList;
-
-mpfr_t ** analyticalSFS_LUT;
-
-void computeAnalyticalSFS(int sequences, FILE * fp);
-void computeAnalyticalSFSExpo(int sequences, double R, FILE * fpSFSo);
-long double xExponential_Integral_Ei( long double x );
-void mpfr_Exponential_Integral_Ei( mpfr_t EImp, mpfr_t xmp );
-#endif
-
-void printHeading (FILE * fp);
-void computeCorrelationMatrixPairwise(alignment_struct * alignment, clr_struct * omega, int omegaIndex, int firstRowIndex, void * threadData, cor_t ** myCorrelationMatrix, char * lookuptable);
-void applyCorrelationMatrixAdditions (clr_struct * omega, int omegaIndex, int firstRowIndex, cor_t ** correlationMatrix);
-void overlapCorrelationMatrixAdditions (alignment_struct * alignment, clr_struct * omega, int lvw_i, int cvw_i, int * firstRowToCopy, int * firstRowToCompute, int * firstRowToAdd);
-void shiftCorrelationMatrixValues (clr_struct * omega, int lvw_i, int cvw_i, int firstRowToCopy, cor_t ** correlationMatrix);
-
-
-void commandLineParser(int argc, char** argv, 
-		       char * infile,
-		       char * sfsfile,
-                       char * sfsofile,
-		       char * sfofile, 
-		       int * grid, 
-                       int * length,                    
-                       unsigned int * seed,
-		       int * fileFormat,	
-		       int * results,
-		       char * outgroupName,
-		       unsigned char *userSetFolded,
-			unsigned char * userSFS,
-			unsigned char * onlySFS,
-			unsigned char * onlySF,
-		       int * monomorphic,
-			int * threads,
-			int * sequences,
-		       int * analyticalSFS,
-		       double *growthRate);
-
-void removeMonomorphicSites (int monomorphic, FILE * fp);
-
-t_sfs computeBaseLikelihood();
-t_sfs getAlpha (int sweepPosition, t_sfs * likelihood);
-
-
-int isBinary(char input);
-
-void printIntArray(int *array, int n);
-
-void printUCharArray(unsigned char *array, int n);
-
-void printFloatArray(float *array, int n);
-
-void printCharArray(char *array, int n);
-
-int isEndOfLine(char ent);
-
-void goToLineEnd(FILE *fp);
-
-int findFirstAlignment(FILE *fp, int format);
-
-int findNextAlignment(FILE *fp, int fileFormat);
-
-void freeAlignment();
-
-void readAlignment(FILE *fp, int format, FILE * fpInfo, FILE * sfO);
-
-void compressAlignment(alignment_struct *alignment);
-
-void knuthShuffle(int orgArray[], int arraySize, int start, int end);
-
-int parseSample(FILE *fp, int targetTok, char **word, int *wordLength, int curTok);
-
-void unGetChars(FILE *fp, char* chars, int n);
-
-int isValidDNACharacter(char input);
-
-void parseIndividual(char *word, char** genotype, char delimiter, int token, char* states, char phased, char unphased, int *ploidy, int *max_ploidy);
-
-void ignoreAll(FILE * fp, char * ent);
-
-int isSpace(char ent);
-
-double XchooseY_ln(int x, int y);
-
-void checkSNIPPositions (FILE* fp, alignment_struct * alignment, int index);
-
-void createSFS (FILE * fpSFS, FILE * fpSFSo, int alignmentIndex, int * SFSsize);
-void createCLR (int grid);
-void createPROBS (int probGrid);
-void createPatterns(void);
-void computeFactLUT(void);
-
-double gettime(void);
-
-t_sfs likelihoodSFS_SNP(t_sfs * tmpSFS, int x, int n, unsigned char f, int c);
-
-void updateSF(FILE * fpSFo);
-
-#ifdef _USE_PTHREADS
-
-typedef struct
-{
-	int threadID;
-	int threadTOTAL;
-
-	int threadBARRIER;
-	int threadOPERATION;
-
-}threadData_t;
-
-pthread_t * workerThreadL;
-threadData_t * threadDataL;
-
-int gridP;
-void likelihoodSFS_thread(int tid, int threads);
-void parallelComputationRVLUT_thread(int tid, int threads);
-void computeAlpha_parallel(int grid);
-void parallelComputationAlpha_thread(int tid, int threads);
-void syncThreadsBARRIER();
-
-
-#endif
-
-#ifdef _DO_CHECKPOINTS
-double lastCheckpointTime;
-double checkPointInterval;
-extern void writeCheckpoint();
-#endif
-
-#endif

debian/changelog

-sweed (3.2.1+dfsg-1) unstable; urgency=medium
+sweed (3.2.1+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #902960)
 

debian/patches/hardening.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 04 Jul 2018 09:47:17 +0200
+Description: Propagate hardening options
+
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -3,7 +3,7 @@
+ 
+ CC = gcc
+ 
+-CFLAGS = -Wall -O3 -g
++CFLAGS += -Wall -O3 -g
+ 
+ LIBRARIES = -lm
+ 
+@@ -14,7 +14,7 @@ OBJS = SweeD.o SweeD_Input.o SweeD_Kerne
+ all: $(EXECNAME)
+ 
+ SweeD : $(OBJS)
+-	$(CC) $(CFLAGS) -o $(EXECNAME) $(OBJS) $(LIBRARIES)
++	$(CC) $(CFLAGS) -o $(EXECNAME) $(OBJS) $(LIBRARIES) $(LDFLAGS)
+ 
+ SweeD.o: SweeD.c 
+ 	$(CC) $(CFLAGS) -c SweeD.c

debian/patches/series

+hardening.patch

debian/rules

@@ -4,7 +4,7 @@
 #export DH_VERBOSE = 1
 
 
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 #export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
 #export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed