Upgrade to samtools 1.14. (#1583)

* Upgrade to samtools 1.14. * Update old CRAM files that samtools no longer accepts.
samtools · Dec 8, 2021 · c0b61a2 · c0b61a2
1 parent e927064
commit c0b61a2
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/scripts/install-samtools.sh b/scripts/install-samtools.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 set -ex
-wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
-tar -xjvf samtools-1.10.tar.bz2
-cd samtools-1.10 && ./configure --prefix=/usr && make && sudo make install
+wget https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2
+tar -xjvf samtools-1.14.tar.bz2
+cd samtools-1.14 && ./configure --prefix=/usr && make && sudo make install
diff --git a/src/test/java/htsjdk/utils/SamtoolsTestUtils.java b/src/test/java/htsjdk/utils/SamtoolsTestUtils.java
@@ -13,7 +13,7 @@
  */
 public class SamtoolsTestUtils {
     private static final String SAMTOOLS_BINARY_ENV_VARIABLE = "HTSJDK_SAMTOOLS_BIN";
-    public final static String expectedSamtoolsVersion = "1.10";
+    public final static String expectedSamtoolsVersion = "1.14";
 
     /**
      * @return true if samtools is available, otherwise false

diff --git a/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram b/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram
diff --git a/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai b/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai