[med-svn] [snap-aligner] 01/01: drop patch of tests/*.py as they are not working and not run

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository snap-aligner.

commit ec9d62485a6b1333fdb16184f39d62e30111aa3c
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Sep 30 11:16:35 2015 -0700

    drop patch of tests/*.py as they are not working and not run
---
 debian/patches/series            |  1 -
 debian/patches/skip-sam-validate | 36 ------------------------------------
 2 files changed, 37 deletions(-)

diff --git a/debian/patches/series b/debian/patches/series
index 573857e..5acb609 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 spelling
 finish-rename
-skip-sam-validate
diff --git a/debian/patches/skip-sam-validate b/debian/patches/skip-sam-validate
deleted file mode 100644
index 111db1f..0000000
--- a/debian/patches/skip-sam-validate
+++ /dev/null
@@ -1,36 +0,0 @@
-Author: Michael R. Crusoe
-Description: skip use of binary Java program
---- snap-aligner.orig/tests/datatest.py
-+++ snap-aligner/tests/datatest.py
-@@ -80,9 +80,9 @@
-             temps.append(outfile)
-             if not ok: continue
-             # validate output
--            ok = runit(["java", "-jar", _f("ValidateSamFile.jar"), "input=" + outfile, "output=" + _f("temp/validate-#")], "validate-#")
--            temps.append(_f("temp/validate-#"))
--            if not ok: continue
-+            #ok = runit(["java", "-jar", _f("ValidateSamFile.jar"), "input=" + outfile, "output=" + _f("temp/validate-#")], "validate-#")
-+            #temps.append(_f("temp/validate-#"))
-+            #if not ok: continue
-             # translate output to sam if needed
-             check_output = outfile
-             if output_format == "bam":
---- snap-aligner.orig/tests/filetest.py
-+++ snap-aligner/tests/filetest.py
-@@ -138,11 +138,11 @@
-                                 failed += 1
-                                 continue
-                             # validate output
--                            ok = runit(["java", "-jar", _f("ValidateSamFile.jar"), "input=" + outfile, "output=" + _f("temp/validate-#")], "validate-#")
--                            temps.append(_f("temp/validate-#"))
--                            if not ok:
--                                failed += 1
--                                continue
-+                            #ok = runit(["java", "-jar", _f("ValidateSamFile.jar"), "input=" + outfile, "output=" + _f("temp/validate-#")], "validate-#")
-+                            #temps.append(_f("temp/validate-#"))
-+                            #if not ok:
-+                            #    failed += 1
-+                            #    continue
-                             if False:
-                                 # todo: need more sophisticated diff
-                                 # remove header, convert to SAM if needed

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