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README
View file @ 298b9413
Standard RAxML version 8.2.11
Standard RAxML version 8.2.12
============================================================================================================
......
axml.c
View file @ 298b9413
......@@ -6601,11 +6601,16 @@ static void get_args(int argc, char *argv[], analdef *adef, tree *tr)
{
printf("All options supported\n");
fprintf(flagCheckFile, "All options supported\n");
}
fclose(flagCheckFile);
exit(0);
}
else
{
fclose(flagCheckFile);
exit(-1);
}
}
if(tr->useAccumulatedEPACutoff && epaSet)
{
......
axml.h
View file @ 298b9413
......@@ -168,9 +168,9 @@
#define PointGamma(prob,alpha,beta) PointChi2(prob,2.0*(alpha))/(2.0*(beta))
#define programName "RAxML"
#define programVersion "8.2.11"
#define programVersionInt 8211
#define programDate "June 2017"
#define programVersion "8.2.12"
#define programVersionInt 8212
#define programDate "May 2018"
#define TREE_EVALUATION 0
......
debian/changelog
View file @ 298b9413
raxml (8.2.12+dfsg-1) unstable; urgency=medium
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Andreas Tille <tille@debian.org> Fri, 08 Jun 2018 10:58:27 +0200
raxml (8.2.11+dfsg-1) unstable; urgency=medium
[ Shamika Mohanan ]
......
debian/control
View file @ 298b9413
......@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
help2man
Standards-Version: 4.1.1
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/raxml.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/raxml.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/raxml
Vcs-Git: https://salsa.debian.org/med-team/raxml.git
Homepage: http://www.exelixis-lab.org/
Package: raxml
......
multiple.c
View file @ 298b9413
......@@ -831,15 +831,15 @@ void doAllInOne(tree *tr, analdef *adef)
break;
case MR_STOP:
printBothOpenMPI("Stopped Rapid BS search after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_STOP:
printBothOpenMPI("Stopped Rapid BS search after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_IGN_STOP:
printBothOpenMPI("Stopped Rapid BS search after %d replicates with MRE_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
default:
assert(0);
......@@ -855,15 +855,15 @@ void doAllInOne(tree *tr, analdef *adef)
break;
case MR_STOP:
printBothOpenMPI("Rapid BS search did not converge after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_STOP:
printBothOpenMPI("Rapid BS search did not converge after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_IGN_STOP:
printBothOpenMPI("Rapid BS search did not converge after %d replicates with MR_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
default:
assert(0);
......@@ -1348,15 +1348,15 @@ void doBootstrap(tree *tr, analdef *adef, rawdata *rdta, cruncheddata *cdta)
break;
case MR_STOP:
printBothOpenMPI("Stopped Standard BS search after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_STOP:
printBothOpenMPI("Stopped Standard BS search after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_IGN_STOP:
printBothOpenMPI("Stopped Standard BS search after %d replicates with MRE_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
default:
assert(0);
......@@ -1372,15 +1372,15 @@ void doBootstrap(tree *tr, analdef *adef, rawdata *rdta, cruncheddata *cdta)
break;
case MR_STOP:
printBothOpenMPI("Standard BS search did not converge after %d replicates with MR-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_STOP:
printBothOpenMPI("Standard BS search did not converge after %d replicates with MRE-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
case MRE_IGN_STOP:
printBothOpenMPI("Standard BS search did not converge after %d replicates with MR_IGN-based Bootstopping criterion\n", bootstrapsPerformed);
printBothOpenMPI("WRF Average of %d random splits: %f\n", adef->bootstopPermutations, pearsonAverage);
printBothOpenMPI("WRF Average of %d random splits: %f %%\n", adef->bootstopPermutations, pearsonAverage);
break;
default:
assert(0);
......
parsePartitions.c
View file @ 298b9413
......@@ -642,7 +642,16 @@ static int myGetline(char **lineptr, int *n, FILE *stream)
return p - *lineptr;
}
static void nonContiguousError(analdef *adef)
{
if(adef->compressPatterns == FALSE)
{
printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
printf("to the same partition model, when pattern compression is disabled via the -H flag,\n");
printf("or when pattern compression is disabled implicitely by some other option that requires it!\n\n");
exit(-1);
}
}
void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
{
......@@ -775,6 +784,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
if(*ch == ',')
{
upper = lower;
nonContiguousError(adef);
goto SINGLE_NUMBER;
}
......@@ -818,6 +828,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
if(*ch == ',')
{
ch++;
nonContiguousError(adef);
goto numberPairs;
}
......@@ -832,13 +843,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
exit(-1);
}
if(adef->compressPatterns == FALSE)
{
printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
printf("to the same partition model, when pattern compression is disabled via the -H flag,\n");
printf("or when pattern compression is disabled implicitely by some other option that requires it!\n\n");
exit(-1);
}
nonContiguousError(adef);
l = 0;
while(isNum(*ch))
......@@ -856,9 +861,11 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
{
goto parsed;
}
if(*ch == ',')
{
ch++;
nonContiguousError(adef);
goto numberPairs;
}
}
......