From 62b6be90354389d3bec8db5bad7fe62dc0e36e06 Mon Sep 17 00:00:00 2001
From: Dennis Hendriksen <d.hendriksen@umcg.nl>
Date: Mon, 7 Sep 2020 08:04:33 +0200
Subject: [PATCH] Fix tsv.gz score conversion

---
 .../capice/vcf/TsvToVcfMapperImpl.java         |   2 +-
 .../java/org/molgenis/capice/vcf/AppIT.java    |  17 +++++++++++++++++
 .../resources/input_precomputed_scores.tsv.gz  | Bin 0 -> 145 bytes
 3 files changed, 18 insertions(+), 1 deletion(-)
 create mode 100644 src/test/resources/input_precomputed_scores.tsv.gz

diff --git a/src/main/java/org/molgenis/capice/vcf/TsvToVcfMapperImpl.java b/src/main/java/org/molgenis/capice/vcf/TsvToVcfMapperImpl.java
index 00ddaca1..730c5267 100644
--- a/src/main/java/org/molgenis/capice/vcf/TsvToVcfMapperImpl.java
+++ b/src/main/java/org/molgenis/capice/vcf/TsvToVcfMapperImpl.java
@@ -134,7 +134,7 @@ private float getPrediction(CSVRecord record) {
   }
 
   private static Reader createInputReader(Path inputTsvPath) throws IOException {
-    if (inputTsvPath.endsWith(".gz")) {
+    if (inputTsvPath.toString().endsWith(".gz")) {
       return new InputStreamReader(
           new GZIPInputStream(new FileInputStream(inputTsvPath.toFile())), UTF_8);
     } else {
diff --git a/src/test/java/org/molgenis/capice/vcf/AppIT.java b/src/test/java/org/molgenis/capice/vcf/AppIT.java
index fc9f61e8..e1c77145 100644
--- a/src/test/java/org/molgenis/capice/vcf/AppIT.java
+++ b/src/test/java/org/molgenis/capice/vcf/AppIT.java
@@ -51,4 +51,21 @@ void testPrecomputedScores() throws IOException {
 
     assertEquals(expected, actual);
   }
+
+  @Test
+  void testPrecomputedScoresGzipped() throws IOException {
+    String inputFile = ResourceUtils.getFile("classpath:input_precomputed_scores.tsv.gz").toString();
+    String outputFile = sharedTempDir.resolve("capice_precomputed_scores_actual.vcf.gz").toString();
+
+    String[] args = {"-i", inputFile, "-o", outputFile, "-f", "-t", "precomputed_scores"};
+    SpringApplication.run(App.class, args);
+
+    String actual = getVcfGzAsString(Path.of(outputFile)).replaceAll("##CAP=.*", "##CAP=test");
+    Path expectedPath = Paths.get("src", "test", "resources", "capice_precomputed_scores.vcf");
+    String expected =
+        Files.readString(expectedPath, StandardCharsets.UTF_8)
+            .replaceAll("\\n|\\r\\n", System.getProperty("line.separator"));
+
+    assertEquals(expected, actual);
+  }
 }
diff --git a/src/test/resources/input_precomputed_scores.tsv.gz b/src/test/resources/input_precomputed_scores.tsv.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d703e851905f8dccb215bc2a41382617ee6cfbe5
GIT binary patch
literal 145
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z3<bcm7E($UJy}ndj>avxh4kOTega`nxep8kstQ@Mrf@Is+T9(!%%JgkYrHnxsAR~P
z5<A(7G$&Fk`@_Iw%3P<h7C}2zfJr<}yRz{=1Am#q6$ML6cl(+HGRIpCwg3PC>svh<

literal 0
HcmV?d00001