[fix]: Replace assert statements with aio assert

Add function aio::doAssert to replace asserts
Did not use aio::assert as name  since aio.h
namespace complains due to assert being a macro
Fixes the major bug explained in #527
Fixes issues #520 #474 #466 #420 #405 #396 #385
Possibly others; other issues should rerun the
commands using the latest version.

.gitignore

@@ -31,6 +31,7 @@
 # Other files
 *.d
 angsd
+angsdput*
 misc/NGSadmix
 misc/contamination
 misc/contamination2

abcAncestry.cpp

@@ -1,4 +1,3 @@
-#include <cassert>
 #include <ctype.h>
 #include "shared.h"
 #include "analysisFunction.h"
@@ -52,7 +51,7 @@ void abcAncestry::clean(funkyPars *pars){
 
 
 void abcAncestry::print(funkyPars *pars){
-  assert(pars->anc!=NULL);
+	aio::doAssert(pars->anc!=NULL,1,AT,"");
   if(doAncestry==1){
 
   }

abcCounts.cpp

@@ -5,7 +5,6 @@
 */
 
 #include <htslib/kstring.h>
-#include <cassert>
 #include "analysisFunction.h"
 #include "abc.h"
 #include "abcCounts.h"
@@ -476,7 +475,7 @@ void abcCounts::print(funkyPars *pars){
     countQs(pars->chk,qsDist,pars->keepSites,minQ);
 
   if(doDepth!=0){
-    assert(pars->counts!=NULL);
+	  aio::doAssert(pars->counts!=NULL,1,AT,"");
     for(int s=0;s<pars->numSites;s++) {
       if(pars->keepSites[s]==0)
 	continue; 
@@ -673,7 +672,7 @@ suint **abcCounts::countNucs(const chunkyT *chk,int *keepSites,int mmin,int mmax
 void abcCounts::run(funkyPars *pars){
   if(doCounts==0)
     return;
-  assert(pars->chk!=NULL&&pars->counts==NULL);
+  aio::doAssert(pars->chk!=NULL&&pars->counts==NULL,1,AT,"");
   pars->counts = countNucs(pars->chk,pars->keepSites,setMinDepthInd,setMaxDepthInd);
   if(doebd){
     counts *cnts = new counts;

abcError.cpp

@@ -1,6 +1,5 @@
 #include <list>
 #include <cmath>
-#include <cassert>
 #include "bfgs.h"
 #include "analysisFunction.h"
 #include "abcError.h"
@@ -420,7 +419,7 @@ void abcError::clean(funkyPars *pars){
 void abcError::run(funkyPars *pars){
   if(doError==0)
     return;
-  assert(pars->counts!=NULL);
+  aio::doAssert(pars->counts!=NULL,1,AT,"");
 
 
   //  pars->opt->emIter=emIter;

abcFilter.cpp

@@ -10,7 +10,6 @@ osome if we have reached the last position from the keep list.
 Maybe there are some memleaks. This will have to be fixed later.
 */
 
-#include <cassert>
 #include <sys/stat.h>
 #include "shared.h"
 #include "abc.h"

abcFreq.cpp

@@ -9,7 +9,6 @@
 
 */
 
-#include <cassert>
 #include <cmath>
 #include <htslib/kstring.h>
 #include <htslib/bgzf.h>
@@ -442,7 +441,7 @@ void abcFreq::print(funkyPars *pars) {
 
       int major = pars->major[s];
       int minor = pars->minor[s];
-      assert(major!=4&&minor!=4);
+	  aio::doAssert(major!=4&&minor!=4,1,AT,"");
 
       for(int i=0;i<3*pars->nInd;i++) {
 	ksprintf(&bufstr, "\t%f",pars->post[s][i]);
@@ -596,7 +595,7 @@ void abcFreq::run(funkyPars *pars) {
     }
   }
   if(doPost) {
-    assert(pars->likes!=NULL);
+	  aio::doAssert(pars->likes!=NULL,1,AT,"");
 
     double **post = new double*[pars->numSites];
     double **like=angsd::get3likes(pars);
@@ -622,7 +621,7 @@ void abcFreq::run(funkyPars *pars) {
 	   fprintf(stderr,"\t-> Problem calling genotypes at: (%s,%d)\n",header->target_name[pars->refId],pars->posi[s]+1);	   
       }
       else if(doPost==4){
-	assert(fl!=NULL);
+		aio::doAssert(fl!=NULL,1,AT,"");
 	//af for this pos: fl->af[pars->posi[s]]
 	//an for this pos: fl->an[pars->posi[s]]
 	//ac for this pos: fl->ac[pars->posi[s]]
@@ -680,7 +679,7 @@ void abcFreq::likeFreq(funkyPars *pars,freqStruct *freq){//method=1: bfgs_known
     loglike= pars->likes;
   else
     loglike=angsd::get3likesRescale(pars);
-  assert(loglike!=NULL);
+  aio::doAssert(loglike!=NULL,1,AT,"");
 
   if(doSNP)
     freq->lrt = new double[pars->numSites];
@@ -1283,7 +1282,7 @@ double abcFreq::emFrequency(double *loglike,int numInds, int iter,double start,i
       break;
     }
     p=-999;
-    assert(p!=999);
+	aio::doAssert(p!=999,1,AT,"");
     return p;
   }
 

abcGetFasta.cpp

@@ -9,7 +9,6 @@
   Actually no need to mutex, except for the first chunk. Lets fix it at some point.
 */
 
-#include <cassert>
 
 #include "analysisFunction.h"
 #include "shared.h"
@@ -137,7 +136,7 @@ char *abcGetFasta::loadChr(perFasta *f, char*chrName,int chrId){
 
 char *abcGetFasta::magic(int refId,int *posi,int numSites,perFasta *f){
   pthread_mutex_lock(&f->aMut);
-  assert(refId!=-1);
+  aio::doAssert(refId!=-1,1,AT,"");
   //load new chr if different from last or if nothing has been loaded before
   if(f->curChr==-1||refId!=f->curChr){
     //    fprintf(stderr,"[%s] chaning to chr: %d\n",__FUNCTION__,refId);

abcIBS.cpp

@@ -6,7 +6,6 @@
   part of angsd
   NB for cov. maf > 0.001 is hardcoded (don't want the world to explode)
 */
-#include <cassert>
 #include <cmath>
 #include <cstdlib>
 #include <htslib/kstring.h>
@@ -268,12 +267,12 @@ void abcIBS::printHaplo(funkyPars *pars){
   if(makeMatrix){
     for(int i=0;i<pars->nInd;i++){
       for(int j=0;j<pars->nInd;j++){
-	assert( haplo->ibsMatrix[i*pars->nInd+j] >= 0  || haplo->nonMis[i*pars->nInd+j] >= 0 );
+	aio::doAssert( haplo->ibsMatrix[i*pars->nInd+j] >= 0  || haplo->nonMis[i*pars->nInd+j] >= 0 ,1,AT,"");
 	//	  fprintf(stdout,"negative count %d\t%d\n",haplo->ibsMatrix[i*pars->nInd+j],haplo->nonMis[i*pars->nInd+j]);
 
 	ibsMatrixAll[i*pars->nInd+j] += haplo->ibsMatrix[i*pars->nInd+j];
 	nonMisAll[i*pars->nInd+j] += haplo->nonMis[i*pars->nInd+j];
-	assert(nonMisAll[i*pars->nInd+j] >= 0  || ibsMatrixAll[i*pars->nInd+j] >= 0);
+	aio::doAssert(nonMisAll[i*pars->nInd+j] >= 0  || ibsMatrixAll[i*pars->nInd+j] >= 0,1,AT,"");
       }
     }
   }

abcMajorMinor.cpp

@@ -28,13 +28,14 @@
 
 
 #include <cmath> //<- for log,exp
-#include <cassert>
 #include <cfloat>
 #include "shared.h"
 #include "analysisFunction.h"
 #include "abc.h"
 #include "abcMajorMinor.h"
 #include "abcFilter.h"
+#include "aio.h"
+
 static int isnaninf(double *d,int l){
   for(int i=0;i<l;i++)
     if(std::isnan(d[i])||std::isinf(d[i]))
@@ -278,7 +279,7 @@ void abcMajorMinor::majorMinorGL(funkyPars *pars,int doMajorMinor){
 	fprintf(stdout,"\t-> Something has gone wrong trying to infer major/minor from GLS at \'%s\' %d will discard site from analysis\n",header->target_name[pars->refId],pars->posi[s]+1);
 	pars->keepSites[s]=0;
       }
-      // assert(choiceMajor!=-1&&choiceMinor!=-1);
+      // aio::doAssert(choiceMajor!=-1&&choiceMinor!=-1);
       for(int i=0;i<pars->nInd;i++){
 	W0=exp(pars->likes[s][i*10+angsd::majorminor[choiceMajor][choiceMajor]])*0.25;
 	W1=exp(pars->likes[s][i*10+angsd::majorminor[choiceMajor][choiceMinor]])*0.5;
@@ -389,7 +390,7 @@ int abcMajorMinor::majorMinorEBD(funkyPars *pars,int doMajorMinor){
 }
 
 void majorMinorCounts(suint **counts,int nFiles,int nSites,char *major,char *minor,int *keepSites,int doMajorMinor,char *ref,char *anc) {
-  assert(counts!=NULL);
+  aio::doAssert(counts!=NULL,1,AT,"");
 
   for(int s=0;s<nSites;s++){
     if(keepSites==0)
@@ -517,7 +518,7 @@ void abcMajorMinor::run(funkyPars *pars){
 	continue;
       int major = pars->major[s];
       int minor = pars->minor[s];
-      assert(major!=4&&minor!=4);
+      aio::doAssert(major!=4&&minor!=4,1,AT,"");
 
       lh3->hasAlloced[s]=1;
       lh3->lh3[s] = new double[3*pars->nInd];

abcMcall.cpp

@@ -1,5 +1,5 @@
-#include <cassert>
 #include "abc.h"
+#include "aio.h"
 #include "analysisFunction.h"
 #include "shared.h"
 #include "abcMcall.h"
@@ -22,7 +22,7 @@ void abcMcall::printArg(FILE *fp){
 }
 
 void offset2allele(int a,int &b,int &c){
-  assert(a>=0&&a<10);
+  aio::doAssert(a>=0&&a<10,1,AT,"");
   if(a==0){//AA
     b=0;
     c=0;
@@ -605,8 +605,8 @@ void abcMcall::run(funkyPars *pars) {
        int b2=refToInt[DAS_BEST[1]];
        //    fprintf(stderr,"offset2allele: which=%d a1=%d a2=%d DAS: b1=%d b2=%d lk: %f nd->l: %d\n",whichmax,a1,a2,b1,b2,gc_llh[i*10+whichmax],pars->chk->nd[s][i]?pars->chk->nd[s][i]->l:0);
        if(b2!=4){
-	 assert(a1==b1||a1==b2);
-	 assert(a2==b1||a2==b2);
+	 aio::doAssert(a1==b1||a1==b2);
+	 aio::doAssert(a2==b1||a2==b2);
        }
        dat->gcdat[s][i] = -1;
        if(pars->chk->nd[s][i]&&pars->chk->nd[s][i]->l>0){

abcScounts.cpp

@@ -1,5 +1,4 @@
 #include <ctype.h>
-#include <cassert>
 #include "shared.h"
 #include "analysisFunction.h"
 #include "abcScounts.h"
@@ -134,7 +133,7 @@ void abcScounts::print(funkyPars *pars){
       cnts.C = pars->counts[s][1];
       cnts.G = pars->counts[s][2];
       cnts.T = pars->counts[s][3];
-      assert(sizeof(counts)==bgzf_write(outfile,&cnts,sizeof(counts)*1));
+      aio::doAssert(sizeof(counts)==bgzf_write(outfile,&cnts,sizeof(counts)*1),1,AT,"");
 
     }
   }