use vcfpp.h v0.4.0

Zilong-Li · Jul 2, 2024 · 9836448 · 9836448
1 parent 99ca8df
commit 9836448
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Showing 3 changed files with 20 additions and 4 deletions.
diff --git a/src/vcf-popgen.cpp b/src/vcf-popgen.cpp
@@ -14,7 +14,7 @@ List heterozygosity(std::string vcffile, std::string region = "", std::string sa
     while (vcf.getNextVariant(var)) {
         if (pass && (var.FILTER() != "PASS")) continue;
         if ((qual > 0) && (var.QUAL() < qual)) continue;
-        var.getGenotypes(gt);
+        if(!var.getGenotypes(gt)) continue;
         // analyze SNP variant
         if (!var.isSNP()) continue;
         assert(var.ploidy() == 2);  // make sure it is diploidy

diff --git a/src/vcf-reader.cpp b/src/vcf-reader.cpp
@@ -190,7 +190,7 @@ class vcfreader {
     }
 
     vector<int> genotypes(bool collapse) {
-        var.getGenotypes(v_int);
+        if (!var.getGenotypes(v_int)) { return vector<int>(); }
         if (var.ploidy() == 2 && collapse) {
             for (size_t i = 0; i < v_int.size(); i += 2) {
                 v_int[i + 1] += v_int[i];

diff --git a/src/vcfpp.h b/src/vcfpp.h
@@ -2,7 +2,7 @@
  * @file        https://github.com/Zilong-Li/vcfpp/vcfpp.h
  * @author      Zilong Li
  * @email       zilong.dk@gmail.com
- * @version     v0.3.9
+ * @version     v0.4.0
  * @breif       a single C++ file for manipulating VCF
  * Copyright (C) 2022-2023.The use of this code is governed by the LICENSE file.
  ******************************************************************************/
@@ -497,7 +497,9 @@ class BcfRecord
         ret = bcf_get_genotypes(header->hdr, line.get(), &gts, &ndst);
         if(ret <= 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "GT not present for current site. did you initilize the variant object?\n";
+#    endif
             return false;
         }
         // if nploidy is not set manually. find the max nploidy using the first variant (eg. 2) resize v as
@@ -568,7 +570,9 @@ class BcfRecord
         ret = bcf_get_genotypes(header->hdr, line.get(), &gts, &ndst);
         if(ret <= 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "GT not present for current site. did you initilize the variant object?\n";
+#    endif
             return false;
         }
         v.resize(ret);
@@ -672,7 +676,7 @@ class BcfRecord
         fmt = bcf_get_fmt(header->hdr, line.get(), tag.c_str());
         if(!fmt)
         {
-            throw std::invalid_argument("invalid FORMAT=" + tag + " for current variant.\n");
+            throw std::invalid_argument("no FORMAT=" + tag + " in the VCF header.\n");
         }
         nvalues = fmt->n;
         // if ndst < (fmt->n+1)*nsmpl; then realloc is involved
@@ -767,8 +771,10 @@ class BcfRecord
         }
         else
         {
+#    if defined(VERBOSE)
             std::cerr << "there are multiple values for " + tag
                              + " in INFO for current site. please use vector instead\n";
+#    endif
             return false;
         }
     }
@@ -825,7 +831,9 @@ class BcfRecord
         }
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
+#    endif
             return false;
         }
         return true;
@@ -861,7 +869,9 @@ class BcfRecord
 
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
+#    endif
             return false;
         }
         return true;
@@ -927,7 +937,9 @@ class BcfRecord
         if(bcf_update_genotypes(header->hdr, line.get(), gt, v.size()) < 0)
         {
             free(gt);
+#    if defined(VERBOSE)
             std::cerr << "couldn't set genotypes correctly.\n";
+#    endif
             return false;
         }
         free(gt);
@@ -994,7 +1006,9 @@ class BcfRecord
 
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set format " + tag + " corectly.\n";
+#    endif
             return false;
         }
         return true;
@@ -1026,7 +1040,9 @@ class BcfRecord
         }
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set format " + tag + " corectly.\n";
+#    endif
             return false;
         }
         return true;