[med-svn] [seqan2] 02/03: Work around GNU Hurd TANDEM problem

[Michael Crusoe]

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misterc-guest pushed a commit to tag debian/2.3.0_0.20161019_af07bc1+dfsg-2
in repository seqan2.

commit b9be45ddec32dfb88396d27948567cbe148d1976
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Thu Oct 20 04:54:54 2016 -0700

    Work around GNU Hurd TANDEM problem
---
 debian/changelog             |  3 ++-
 debian/patches/series        |  1 +
 debian/patches/tandem-rename | 54 ++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 57 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index ad46f7d..8f9b4af 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,11 @@
 seqan2 (2.3.0~0.20161019~af07bc1+dfsg-2) experimental; urgency=medium
 
   * Fix typo from upstream's patch.
+  * Work around GNU Hurd TANDEM problem
 
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Thu, 20 Oct 2016 04:48:11 -0700
 
-seqan2 (2.3.0~0.20161019~af07bc1+dfsg-1) experimental; urgency=medium
+seqan2 (2.3.0~0.201610100~af07bc1+dfsg+1) experimental; urgency=medium
 
   * Second experimental build to test fix for #840030. Source from
     https://github.com/seqan/seqan/pull/1887/commits/af07bc19087e662117b70d733e963a1611aa9b9a
diff --git a/debian/patches/series b/debian/patches/series
index be5f91c..94e4c15 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+tandem-rename
 typo-fix
 spelling.patch
 short-description
diff --git a/debian/patches/tandem-rename b/debian/patches/tandem-rename
new file mode 100644
index 0000000..50e626c
--- /dev/null
+++ b/debian/patches/tandem-rename
@@ -0,0 +1,54 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Work around GNU Hurd's TANDEM constant
+https://fossies.org/dox/glibc-2.24/sysdeps_2mach_2hurd_2bits_2ioctls_8h.html#aea2b0b2a11b94d258198cd2104bc79a4
+--- seqan2.orig/apps/gustaf/msplazer.h
++++ seqan2/apps/gustaf/msplazer.h
+@@ -134,7 +134,7 @@
+         INSERTION,          // 1
+         DELETION,           // 2
+         INVERSION,          // 3
+-        TANDEM,             // 4
++        SEQAN_TANDEM,       // 4  TANDEM is an IOCTL numeric constant in Hurd
+         DISPDUPLICATION,    // 5
+         INTERTRANSLOCATION, // 6
+         TRANSLOCATION,      // 7
+@@ -696,7 +696,7 @@
+         case TBreakpoint::INVERSION:
+         out << "SVType: inversion";
+         break;
+-        case TBreakpoint::TANDEM:
++        case TBreakpoint::SEQAN_TANDEM:
+         out << "SVType: tandem";
+         break;
+         case TBreakpoint::DISPDUPLICATION:
+--- seqan2.orig/apps/gustaf/msplazer_algorithms.h
++++ seqan2/apps/gustaf/msplazer_algorithms.h
+@@ -493,7 +493,7 @@
+                     // Double overlap check (not handled jet)
+                     // std::cerr << "double overlap in reference and read called from read overlap" << std::endl;
+                     // std::cout << "Translocation double overlap" << std::endl;
+-                    bp.svtype = TBreakpoint::TANDEM;
++                    bp.svtype = TBreakpoint::SEQAN_TANDEM;
+                 }
+ 
+                 //std::cout << "Breakpoint " << bp << std::endl;
+--- seqan2.orig/apps/gustaf/msplazer_out.h
++++ seqan2/apps/gustaf/msplazer_out.h
+@@ -196,7 +196,7 @@
+         case TBreakpoint::INVERSION:
+         record.type = "inversion";
+         break;
+-        case TBreakpoint::TANDEM:
++        case TBreakpoint::SEQAN_TANDEM:
+         record.type = "tandem";
+         break;
+         case TBreakpoint::DISPDUPLICATION:
+@@ -647,7 +647,7 @@
+         case TBreakpoint::INVERSION:
+         _fillVcfRecordInversion(record, bp, ref, id);
+         return 1;
+-        case TBreakpoint::TANDEM:
++        case TBreakpoint::SEQAN_TANDEM:
+         _fillVcfRecordTandem(record, bp, ref, id);
+         return 1;
+         case TBreakpoint::DISPDUPLICATION:

-- 
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