--sort-vars forced-QUAL/FILTER segfault fix

chrchang · Dec 4, 2024 · 4b29cbd · 4b29cbd
1 parent 5eab376
commit 4b29cbd
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Showing 4 changed files with 11 additions and 11 deletions.
diff --git a/2.0/Tests/TEST_ONE_WAY_EXPORT/run_tests.sh b/2.0/Tests/TEST_ONE_WAY_EXPORT/run_tests.sh
@@ -6,11 +6,11 @@ set -exo pipefail
 # manually-sanity-checked ground truth files.
 
 $1/plink2 $2 $3 --pfile all_ploidy vzs --snps-only --export phylip --out plink2_test
-plink2 --zd plink2_test.phy.want.zst > plink2_test.phy.want
+$1/plink2 --zd plink2_test.phy.want.zst > plink2_test.phy.want
 diff -q plink2_test.phy plink2_test.phy.want
 $1/plink2 $2 $3 --pfile all_ploidy vzs --chr PAR1,X,PAR2 --keep-females --snps-only --export phylip-phased --out plink2_test.phased
-plink2 --zd plink2_test.phased.phy.want.zst > plink2_test.phased.phy.want
+$1/plink2 --zd plink2_test.phased.phy.want.zst > plink2_test.phased.phy.want
 diff -q plink2_test.phased.phy plink2_test.phased.phy.want
 $1/plink2 $2 $3 --pfile all_ploidy vzs --export A --out plink2_test
-plink2 --zd plink2_test.raw.want.zst > plink2_test.raw.want
+$1/plink2 --zd plink2_test.raw.want.zst > plink2_test.raw.want
 diff -q plink2_test.raw plink2_test.raw.want
diff --git a/2.0/Tests/TEST_PHASED_VCF/run_tests.sh b/2.0/Tests/TEST_PHASED_VCF/run_tests.sh
@@ -132,7 +132,7 @@ plink --bfile plink1_data --clump plink2_glm_dbl.PHENO1.glm.logistic --clump-snp
 # ($12 != "") check needed because plink 1.x puts two blank lines at the end of
 # the .clumped file.
 cat plink1_test.clumped | tail -n +2 | awk '{if ($12 == "NONE") $12 = "."; if ($12 != "") print $3"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' > plink1_test.clump_compare
-plink2 --bfile plink1_data --clump cols=+f plink2_glm_dbl.PHENO1.glm.logistic --clump-p1 0.1 --clump-p2 0.2 --out plink2_test
+$1/plink2 --bfile plink1_data --clump cols=+f plink2_glm_dbl.PHENO1.glm.logistic --clump-p1 0.1 --clump-p2 0.2 --out plink2_test
 cat plink2_test.clumps | tail -n +2 | awk '{print $3"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' > plink2_test.clump_compare
 diff -q plink1_test.clump_compare plink2_test.clump_compare
 
@@ -141,7 +141,7 @@ $1/plink2 $2 $3 --bfile plink1_data --maf 0.02 --pheno pheno_qt.txt --glm allow-
 python3 glm_compare.py -1 plink1_glm.assoc.linear -2 plink2_glm.PHENO1.glm.linear -t 0.1
 plink --bfile plink1_data --clump plink2_glm.PHENO1.glm.linear --clump-snp-field ID --clump-p1 0.1 --clump-p2 0.2 --out plink1_test
 cat plink1_test.clumped | tail -n +2 | awk '{if ($12 == "NONE") $12 = "."; if ($12 != "") print $3"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' > plink1_test.clump_compare
-plink2 --bfile plink1_data --clump cols=+f plink2_glm.PHENO1.glm.linear --clump-p1 0.1 --clump-p2 0.2 --out plink2_test
+$1/plink2 --bfile plink1_data --clump cols=+f plink2_glm.PHENO1.glm.linear --clump-p1 0.1 --clump-p2 0.2 --out plink2_test
 cat plink2_test.clumps | tail -n +2 | awk '{print $3"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' > plink2_test.clump_compare
 diff -q plink1_test.clump_compare plink2_test.clump_compare
 
@@ -167,7 +167,7 @@ python3 glm_compare.py -1 plink1_glm.assoc.linear -2 plink2_glm.PHENO1.glm.linea
 $1/plink2 $2 $3 --bfile plink1_data --maf 0.02 --pheno pheno_qt.txt --glm hide-covar --covar plink2_pca.eigenvec --out plink2_glm
 plink --bfile plink1_data --clump plink2_glm.PHENO1.glm.linear --clump-snp-field ID --clump-p1 0.1 --clump-p2 0.2 --out plink1_test
 cat plink1_test.clumped | tail -n +2 | awk '{if ($12 == "NONE") $12 = "."; if ($12 != "") print $3"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' > plink1_test.clump_compare
-plink2 --bfile plink1_data --clump cols=+f plink2_glm.PHENO1.glm.linear --clump-p1 0.1 --clump-p2 0.2 --out plink2_test
+$1/plink2 --bfile plink1_data --clump cols=+f plink2_glm.PHENO1.glm.linear --clump-p1 0.1 --clump-p2 0.2 --out plink2_test
 cat plink2_test.clumps | tail -n +2 | awk '{print $3"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12}' > plink2_test.clump_compare
 diff -q plink1_test.clump_compare plink2_test.clump_compare
 

diff --git a/2.0/plink2.cc b/2.0/plink2.cc
@@ -44,7 +44,7 @@
 namespace plink2 {
 #endif
 
-static const char ver_str[] = "PLINK v2.0.0-a.6.2"
+static const char ver_str[] = "PLINK v2.0.0-a.6.3"
 #ifdef NOLAPACK
   "NL"
 #elif defined(LAPACK_ILP64)
@@ -72,10 +72,10 @@ static const char ver_str[] = "PLINK v2.0.0-a.6.2"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (24 Nov 2024)";
+  " (3 Dec 2024)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
-  ""
+  " "
 
 #ifdef NOLAPACK
 #elif defined(LAPACK_ILP64)

diff --git a/2.0/plink2_data.cc b/2.0/plink2_data.cc
@@ -8902,7 +8902,7 @@ PglErr WritePvarResortedInterval(const ChrInfo* write_cip, const uint32_t* varia
 
       if (write_qual) {
         *cswritep++ = '\t';
-        if (!IsSet(qual_present, variant_uidx)) {
+        if ((!qual_present) || (!IsSet(qual_present, variant_uidx))) {
           *cswritep++ = '.';
         } else {
           cswritep = ftoa_g(quals[variant_uidx], cswritep);
@@ -8911,7 +8911,7 @@ PglErr WritePvarResortedInterval(const ChrInfo* write_cip, const uint32_t* varia
 
       if (write_filter) {
         *cswritep++ = '\t';
-        if (!IsSet(filter_present, variant_uidx)) {
+        if ((!filter_present) || (!IsSet(filter_present, variant_uidx))) {
           *cswritep++ = '.';
         } else if (!IsSet(filter_npass, variant_uidx)) {
           cswritep = strcpya_k(cswritep, "PASS");