diff options
| -rw-r--r-- | RELEASE-NOTES.md | 11 | ||||
| -rw-r--r-- | src/version.h | 4 | ||||
| -rwxr-xr-x | test/dev_test_suite.sh | 1 | ||||
| -rwxr-xr-x | test/lengthy_test_suite.sh | 1 | ||||
| -rwxr-xr-x | test/test_suite.sh | 5 |
5 files changed, 17 insertions, 5 deletions
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md index 946774d..36243c1 100644 --- a/RELEASE-NOTES.md +++ b/RELEASE-NOTES.md @@ -11,6 +11,15 @@ Maintenance release * Fix Travis build with gcc 5.5 (OpenBLAS related round-offs) * Fix Travis build on OSX (brew related) * GEMMA installs on FreeBSD (thanks @outpaddling) +* Added github issue templates to ascertain the github issue + tracker is only used for reporting bugs +* Added more debug output creating the GRM +* Remove info on the floating point version (gemmaf). +* Sane randomization handling: GEMMA now honours the -seed option + (mostly for bslmm). It also allows GSL_RNG_SEED and GSL_RNG_TYPE to + be used. See the + [docs](https://www.gnu.org/software/gsl/doc/html/rng.html). +* The tests now use a fixed seed for the randomizer ## ChangeLog v0.98.2 (2019/05/28) @@ -24,7 +33,7 @@ GCC 10.1 fix release Bug fix release -* Fixes regression on Plink analysis with missing data (thank you @voichek) +* Fixes regression on Plink analysis with missing data #188 (thank you @voichek) To install the image, download and diff --git a/src/version.h b/src/version.h index 6c22a1b..6492b1a 100644 --- a/src/version.h +++ b/src/version.h @@ -1,5 +1,5 @@ // version.h generated by GEMMA scripts/gen_version_info.sh #define GEMMA_VERSION "0.98.3" -#define GEMMA_DATE "2020-09-29" +#define GEMMA_DATE "2020-11-28" #define GEMMA_YEAR "2020" -#define GEMMA_PROFILE "/gnu/store/a7a35vv75zk9k23k8ws4v2wrs123dln1-profile" +#define GEMMA_PROFILE "" diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 0e36218..903c72f 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -3,6 +3,7 @@ gemma=../bin/gemma # gemmaopts="-debug -strict" gemmaopts="-debug -check" +export GSL_RNG_SEED=100 testLinearModel() { $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ diff --git a/test/lengthy_test_suite.sh b/test/lengthy_test_suite.sh index 231475e..6e93220 100755 --- a/test/lengthy_test_suite.sh +++ b/test/lengthy_test_suite.sh @@ -3,6 +3,7 @@ # Long running tests go here gemma=../bin/gemma +export GSL_RNG_SEED=100 testPlinkStandardRelatednessMatrixK() { testname=testPlinkStandardRelatednessMatrixK diff --git a/test/test_suite.sh b/test/test_suite.sh index a598cd2..cc244c0 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -2,6 +2,7 @@ gemma=../bin/gemma gemmaopts="-debug" +export GSL_RNG_SEED=10 testBslmm1() { outn=mouse_hs1940_CD8_bslmm @@ -72,10 +73,10 @@ testBslmm5() { -epm ./output/mouse_hs1940_CD8_bslmm_cc1.param.txt \ -emu ./output/mouse_hs1940_CD8_bslmm_cc1.log.txt \ -predict \ - -o $outn + -o $outn -seed 100 assertEquals 0 $? outfn=output/$outn.prdt.txt - assertEquals "550.67" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals "571.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } testCenteredRelatednessMatrixKFullLOCO1() { |