fix vcfreader and tests

Zilong-Li · Jun 28, 2024 · 4973704 · 4973704
1 parent 6f7ba58
commit 4973704
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Showing 2 changed files with 18 additions and 5 deletions.
diff --git a/src/vcf-reader.cpp b/src/vcf-reader.cpp
@@ -197,7 +197,10 @@ class vcfreader {
     }
 
     vector<int> formatInt(std::string tag) {
-        var.getFORMAT(tag, v_int);
+        if (!var.getFORMAT(tag, v_int)) {
+            vector<int> vna;
+            return vna;
+        }
         int nvals = v_int.size() / br.nsamples;  // how many values per sample
         for (int i = 0; i < br.nsamples; i++) {
             for (int j = 0; j < nvals; j++)
@@ -211,7 +214,7 @@ class vcfreader {
 
     vector<double> formatFloat(std::string tag) {
         vector<double> vecd;
-        var.getFORMAT(tag, v_float);
+        if (!var.getFORMAT(tag, v_float)) return vecd;
         int nvals = v_float.size() / br.nsamples;  // how many values per sample
         vecd.resize(v_float.size());
         for (int i = 0; i < br.nsamples; i++) {
@@ -226,7 +229,10 @@ class vcfreader {
     }
 
     vector<std::string> formatStr(std::string tag) {
-        var.getFORMAT(tag, v_str);
+        if (!var.getFORMAT(tag, v_str)) {
+            vector<std::string> vstr;
+            return vstr;
+        }
         return v_str;
     }
 

diff --git a/tests/testthat/test-vcf-reader.R b/tests/testthat/test-vcf-reader.R
@@ -181,13 +181,20 @@ test_that("vcfreader: read and output variant", {
 
 test_that("vcfreader: remove tag from FORMAT", {
   br <- vcfreader$new(vcffile)
-  br$variant()
+  br$variant()  ## first variant
   s <- unlist(strsplit(br$line(), "\t"))
   expect_identical(s[9], "GT:AD:DP:GQ:PL")
+  br$variant()  ## second variant
   br$rmFormatTag("AD")
+  br$rmFormatTag("AB")
+  br$rmFormatTag("PGT")
+  br$rmFormatTag("PID")
   s <- unlist(strsplit(br$line(), "\t"))
   expect_identical(s[9], "GT:DP:GQ:PL")
-  expect_error(br$formatInt("AD"))
+  expect_identical(s[10], "1/1:2:6:64,6,0")
+  ## AD was removed, so we get integer(0)
+  ad <- br$formatInt("AD") 
+  expect_identical(length(ad),0L)
   ## output current variant to another vcf
   outvcf <- file.path(tempdir(), "test.vcf.gz")
   file.create(outvcf)