[med-svn] [snap-aligner] 01/04: hack around misplaced files from upstream

[Michael Crusoe]

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

commit 88356cc7eb79994caf26923309abe34ee7b80568
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Tue Sep 29 22:16:35 2015 -0700

    hack around misplaced files from upstream
---
 debian/changelog                 |  2 +-
 debian/copyright                 |  7 ++++---
 debian/patches/series            |  1 +
 debian/patches/skip-sam-validate | 36 ++++++++++++++++++++++++++++++++++++
 4 files changed, 42 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 187abae..7d10064 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-snap-aligner (0.18~1.0~beta.18-1) UNRELEASED; urgency=low
+snap-aligner (0.18~1.0~beta.18+dfsg1-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #800340)
 
diff --git a/debian/copyright b/debian/copyright
index 72f1be8..5b21488 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,9 +1,10 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: SNAP
 Source: https://github.com/amplab/snap
-Files-Excluded: import/z*,
-                tests/bin/*.exe
-                tests/bin/*.dll
+Files-Excluded: import/z*
+                tests/bin*
+                tests/datatest/ValidateSamFile.jar
+                import/pdclibhdfs/src/*.xml
 
 Files: *
 Copyright: 2012, Regents of the University of California.
diff --git a/debian/patches/series b/debian/patches/series
index 5acb609..573857e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 spelling
 finish-rename
+skip-sam-validate
diff --git a/debian/patches/skip-sam-validate b/debian/patches/skip-sam-validate
new file mode 100644
index 0000000..111db1f
--- /dev/null
+++ b/debian/patches/skip-sam-validate
@@ -0,0 +1,36 @@
+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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