[med-svn] [pbsuite] 03/05: Add dependency on intervaltree-bio to restore PBHoney's ComplexResolver

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository pbsuite.

commit 17be580ac7bf8a15c31e8544c5908f24eec618be
Author: Afif Elghraoui <afif at debian.org>
Date:   Wed Dec 28 22:31:48 2016 -0800

    Add dependency on intervaltree-bio to restore PBHoney's ComplexResolver
---
 debian/control                                  |  1 +
 debian/patches/rm-intervaltree-dependency.patch | 39 -------------------------
 debian/patches/series                           |  1 -
 3 files changed, 1 insertion(+), 40 deletions(-)

diff --git a/debian/control b/debian/control
index 75c3691..d802827 100644
--- a/debian/control
+++ b/debian/control
@@ -69,6 +69,7 @@ Depends:
 	python-networkx,
 	python-h5py (>= 2.0.1),
 	python-numpy,
+	python-intervaltree-bio,
 	blasr (>= 5.3),
 	samtools,
 Recommends:
diff --git a/debian/patches/rm-intervaltree-dependency.patch b/debian/patches/rm-intervaltree-dependency.patch
deleted file mode 100644
index 4d2b43d..0000000
--- a/debian/patches/rm-intervaltree-dependency.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-Description: Disable ComplexResolver while intervaltree-bio isn't yet in Debian
- See ITP #807803. It's currently held up by Python3.5 incompatibility in
- its dependency python-intervaltree.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2016-02-08
---- pbsuite.orig/pbsuite/honey/__init__.py
-+++ pbsuite/pbsuite/honey/__init__.py
-@@ -1 +1 @@
--__all__ = ["bampie", "Honey", "TGraf", "HSpots", "Force", "ComplexResolver", "massivePhrap"]
-+__all__ = ["bampie", "Honey", "TGraf", "HSpots", "Force", "massivePhrap"]
---- pbsuite.orig/pbsuite/honey/Honey.py
-+++ pbsuite/pbsuite/honey/Honey.py
-@@ -2,15 +2,14 @@
- 
- import argparse, sys
- from pbsuite.utils.setupLogging import *
--from pbsuite.honey import bampie, TGraf, HSpots, Force, ComplexResolver, \
-+from pbsuite.honey import bampie, TGraf, HSpots, Force, \
-                          massivePhrap
- 
- STAGES = {"pie":   bampie.run, \
-           "tails": TGraf.run, \
-           "spots": HSpots.run, \
-           "force": Force.run , \
--          "asm":  massivePhrap.run, \
--          "cpxres": ComplexResolver.run}
-+          "asm":  massivePhrap.run}
- 
- USAGE = """\
-    Honey - genomic variant calling with long sequencing reads
-@@ -21,7 +20,6 @@
-      spots      Find genomic variants within reads' spans.
-      force      Given a BedFile of predicted variants, force search for matching
-      asm        Assemble reads around a variant and remap contigs to a reference
--     cpxres     Complex multi-break-point resolution (beta)
-     
-    See HoneyReadme.txt for documentation or --help for details\
- """
diff --git a/debian/patches/series b/debian/patches/series
index a46d2d0..c436cce 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,5 @@
 fix-syntax-error.patch
 intervaltree-import-statement.patch
-rm-intervaltree-dependency.patch
 fix-example.patch
 fix-shebang-lines.patch
 blasr-5.patch

-- 
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