From 8ae1ab485a598b42fa4ce79f29844884a589cc3d Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Sun, 21 Jan 2018 03:29:41 +0000
Subject: [PATCH 1/3] bump plugin to get scala-reflect version fix

---
 .travis.yml         | 4 ++--
 project/plugins.sbt | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 74ab082..7922c35 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,7 +4,7 @@ jdk:
   - oraclejdk8
 
 scala:
-  - 2.11.8
+  - 2.11.12
 
 script: sbt ++$TRAVIS_SCALA_VERSION clean test
 
@@ -14,7 +14,7 @@ cache:
   - $HOME/.sbt/boot/
   - $HOME/.zinc
 
-after_success: sbt ++$TRAVIS_SCALA_VERSION travis-report
+after_success: sbt ++$TRAVIS_SCALA_VERSION travisReport
 
 before_cache:
   # Tricks to avoid unnecessary cache updates
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 9dc0442..0003a9d 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab.sbt" % "base" % "4.1.0")
+addSbtPlugin("org.hammerlab.sbt" % "base" % "4.2.0")

From b12e1e2237ccc420128c7be0a338c8af5ba93e99 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Sun, 21 Jan 2018 20:08:10 +0000
Subject: [PATCH 2/3] make Strict contig clear() function public

---
 .../scala/org/hammerlab/genomics/reference/ContigName.scala     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/hammerlab/genomics/reference/ContigName.scala b/src/main/scala/org/hammerlab/genomics/reference/ContigName.scala
index 115e795..ac00d84 100644
--- a/src/main/scala/org/hammerlab/genomics/reference/ContigName.scala
+++ b/src/main/scala/org/hammerlab/genomics/reference/ContigName.scala
@@ -103,7 +103,7 @@ object ContigName {
   implicit object Strict extends Factory {
 
     // Exposed for testing
-    private[reference] def clear(): Unit = {
+    def clear(): Unit = {
       seenChrsOpt = None
       names.clear()
     }

From bc049429d79a9cc67ad73242a4549851f6e33c5a Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Sun, 21 Jan 2018 20:50:19 +0000
Subject: [PATCH 3/3] tweak travis coveralls config

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 7922c35..10fe5ce 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ jdk:
 scala:
   - 2.11.12
 
-script: sbt ++$TRAVIS_SCALA_VERSION clean test
+script: sbt ++$TRAVIS_SCALA_VERSION clean coverageTest
 
 cache:
   directories: