Steps to build a patched htsjdk-2.8.1-gs.jar:
1. Checkout htsjdk-2.8.1
git clone https://github.com/samtools/htsjdk.git .
git checkout 2.8.1
2. Apply PR #801
git remote add cmnbroad git@github.com:cmnbroad/htsjdk.git
git fetch cmnbroad
git checkout cmnbroad/cn_cram_md5
3. Fix a bug in src/main/java/htsjdk/samtools/SamReaderFactory.java
-                if (type == InputResource.Type.SEEKABLE_STREAM || type == InputResource.Type.URL) {
+                if (type == InputResource.Type.SEEKABLE_STREAM || type == InputResource.Type.PATH || type == InputResource.Type.URL) {
4. Build
./gradlew clean jar
