From 6fc8b04b4a63f5dfd07bdcfaf7197547f45eeaaa Mon Sep 17 00:00:00 2001
From: Gabriele Sales <gbrsales@gmail.com>
Date: Tue, 11 Feb 2020 14:11:00 +0100
Subject: [PATCH] Depend on salmon 0.7.2

---
 deps/deps.yaml          | 11 ++++-------
 lib/transrate/salmon.rb |  3 ++-
 test/test_salmon.rb     |  2 +-
 3 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/deps/deps.yaml b/deps/deps.yaml
index 956dc53..89de45c 100644
--- a/deps/deps.yaml
+++ b/deps/deps.yaml
@@ -25,22 +25,19 @@ salmon:
   libraries:
     - libgcc_s.so.1
     - libgomp.so.1
+    - liblzma.so.0
     - libm.so.6
     - librt.so.1
-    - libstdc++.so.6
     - libtbb.so
     - libtbb.so.2
     - libtbbmalloc.so
     - libtbbmalloc.so.2
     - libtbbmalloc_proxy.so
     - libtbbmalloc_proxy.so.2
-    - libtbb.dylib
-    - libtbbmalloc.dylib
-    - libtbbmalloc_proxy.dylib
   version:
-    number: '0.6.0'
+    number: '0.7.2'
     command: 'salmon -v'
   url:
     64bit:
-      linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.6.0/SalmonBeta-0.6.0_DebianSqueeze.tar.gz
-      macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.6.0/SalmonBeta-0.6.0_OSX_10.11.tar.gz
+      linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.7.2/Salmon-0.7.2_linux_x86_64.tar.gz
+      macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.7.2/Salmon-0.7.2_OSX_10.11.tar.gz
diff --git a/lib/transrate/salmon.rb b/lib/transrate/salmon.rb
index 4bc8a4d..496253e 100644
--- a/lib/transrate/salmon.rb
+++ b/lib/transrate/salmon.rb
@@ -45,7 +45,8 @@ def build_command assembly, bamfile, threads=4
       cmd << " --sampleUnaligned" # thanks Rob!
       cmd << " --output ."
       cmd << " --useErrorModel"
-      cmd << " --biasCorrect"
+      cmd << " --seqBias"
+      cmd << " --gcBias"
       cmd << " --noEffectiveLengthCorrection"
       cmd << " --useFSPD"
       cmd
diff --git a/test/test_salmon.rb b/test/test_salmon.rb
index 05842c7..722b0dd 100644
--- a/test/test_salmon.rb
+++ b/test/test_salmon.rb
@@ -37,7 +37,7 @@ class TestSalmon < MiniTest::Test
       test = "quant --libType IU --alignments alignments.bam "
       test << "--targets assembly.fa --threads 4 --sampleOut "
       test << "--sampleUnaligned --output . --useErrorModel "
-      test << "--biasCorrect --noEffectiveLengthCorrection --useFSPD"
+      test << "--seqBias --gcBias --noEffectiveLengthCorrection --useFSPD"
       assert_equal test, cmd, "cmd is wrong"
     end