Remove mvicuna, vphaser from tree

Change some db file tests from exact compare to md5 Novoalign ndx build always changes
broadinstitute · Aug 28, 2017 · bdf3995 · bdf3995
1 parent b985ebb
commit bdf3995
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Showing 75 changed files with 11 additions and 15,679 deletions.
diff --git a/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.idx b/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.idx
diff --git a/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.idx.md5 b/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.idx.md5
@@ -0,0 +1 @@
+2e9748024dabadd49dc0862aae5f7180
diff --git a/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.ss b/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.ss
diff --git a/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.ss.md5 b/test/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.ss.md5
@@ -0,0 +1 @@
+143908e3c1d360f5c3f1dae078a8f811
diff --git a/test/input/TestLastalDbBuild/expected/TestLastalDbBuild.suf b/test/input/TestLastalDbBuild/expected/TestLastalDbBuild.suf
diff --git a/test/input/TestLastalDbBuild/expected/TestLastalDbBuild.suf.md5 b/test/input/TestLastalDbBuild/expected/TestLastalDbBuild.suf.md5
@@ -0,0 +1 @@
+38fa84aa28cd468b7dd789906a6db721
diff --git a/test/input/TestToolNovoalign/ebola_expected.nix b/test/input/TestToolNovoalign/ebola_expected.nix
diff --git a/test/unit/test_taxon_filter.py b/test/unit/test_taxon_filter.py
@@ -182,15 +182,15 @@ def test_bmtagger_db_build(self):
         args.func_main(args)
 
         for ext in [
-            ".bitmask", ".srprism.amp", ".srprism.idx", ".srprism.imp", ".srprism.pmp", ".srprism.rmp",
-            ".srprism.ss", ".srprism.ssa", ".srprism.ssd"
+            ".bitmask", ".srprism.amp", ".srprism.imp", ".srprism.pmp", ".srprism.rmp",
+            ".srprism.ssa", ".srprism.ssd"
         ]:
             assert_equal_contents(
                 self, os.path.join(tempDir, output_prefix + ext),
                 os.path.join(myInputDir, "expected", output_prefix + ext)
             )
 
-        for ext in [".srprism.map"]:
+        for ext in [".srprism.map", ".srprism.idx", ".srprism.ss"]:
             assert_md5_equal_to_line_in_file(self, os.path.join(tempDir, output_prefix + ext), os.path.join(myInputDir, "expected", output_prefix + ext+".md5"))
 
 
@@ -217,12 +217,14 @@ def test_lastal_db_build(self):
         )
         args.func_main(args)
 
-        for ext in [".bck", ".des", ".prj", ".sds", ".ssp", ".suf", ".tis"]:
+        for ext in [".bck", ".des", ".prj", ".sds", ".ssp", ".tis"]:
             assert_equal_contents(
                 self, os.path.join(tempDir, output_prefix + ext),
                 os.path.join(myInputDir, "expected", output_prefix + ext)
             )
 
+        for ext in [".suf"]:
+            assert_md5_equal_to_line_in_file(self, os.path.join(tempDir, output_prefix + ext), os.path.join(myInputDir, "expected", output_prefix + ext+".md5"))
 
 class TestDepleteBlastnBam(TestCaseWithTmp):
     '''

diff --git a/test/unit/test_tools_novoalign.py b/test/unit/test_tools_novoalign.py
@@ -9,7 +9,7 @@
 import tools.novoalign
 import tools.samtools
 import pysam
-from test import TestCaseWithTmp
+from test import TestCaseWithTmp, assert_md5_equal_to_line_in_file
 
 
 class TestToolNovoalign(TestCaseWithTmp):
@@ -26,6 +26,7 @@ def test_index(self):
         shutil.copyfile(orig_ref, inRef)
         self.novoalign.index_fasta(inRef)
         outfile = inRef[:-6] + '.nix'
+
         self.assertTrue(os.path.isfile(outfile))
         self.assertTrue(os.path.getsize(outfile))
 

diff --git a/tools/binaries/V-Phaser-2.0/MacOSX/libgomp.1.dylib b/tools/binaries/V-Phaser-2.0/MacOSX/libgomp.1.dylib
diff --git a/tools/binaries/V-Phaser-2.0/MacOSX/variant_caller b/tools/binaries/V-Phaser-2.0/MacOSX/variant_caller
diff --git a/tools/binaries/V-Phaser-2.0/TestData/4528.454.indelRealigned.bam b/tools/binaries/V-Phaser-2.0/TestData/4528.454.indelRealigned.bam
diff --git a/tools/binaries/V-Phaser-2.0/TestData/4528.454.indelRealigned.bam.bti b/tools/binaries/V-Phaser-2.0/TestData/4528.454.indelRealigned.bam.bti
diff --git a/tools/binaries/V-Phaser-2.0/TestData/output/V4528_assembly.covplot.R b/tools/binaries/V-Phaser-2.0/TestData/output/V4528_assembly.covplot.R
diff --git a/tools/binaries/V-Phaser-2.0/TestData/output/V4528_assembly.fdr.var.txt b/tools/binaries/V-Phaser-2.0/TestData/output/V4528_assembly.fdr.var.txt
diff --git a/tools/binaries/V-Phaser-2.0/TestData/output/V4528_assembly.nofdr.var.txt b/tools/binaries/V-Phaser-2.0/TestData/output/V4528_assembly.nofdr.var.txt