[med-svn] [nanopolish] 07/08: Fix compatibility with fast5 0.5.6

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository nanopolish.

commit 9accad76ca987606d1481dc01e2f0cb26d067fe3
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Aug 11 23:22:49 2016 -0700

    Fix compatibility with fast5 0.5.6
---
 debian/patches/fast5-0.5.6.patch | 33 +++++++++++++++++++++++++++++++++
 debian/patches/series            |  1 +
 2 files changed, 34 insertions(+)

diff --git a/debian/patches/fast5-0.5.6.patch b/debian/patches/fast5-0.5.6.patch
new file mode 100644
index 0000000..4bffb27
--- /dev/null
+++ b/debian/patches/fast5-0.5.6.patch
@@ -0,0 +1,33 @@
+Description: Fix compatibility with fast5 0.5.6
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: https://github.com/jts/nanopolish/pull/61
+Last-Update: 2016-08-11
+--- nanopolish.orig/src/nanopolish_squiggle_read.cpp
++++ nanopolish/src/nanopolish_squiggle_read.cpp
+@@ -119,7 +119,7 @@
+         }
+     }
+ 
+-    read_sequence = f_p->get_basecall_seq(basecall_group, read_type);
++    read_sequence = f_p->get_basecall_seq(read_type, basecall_group);
+ 
+     // Load PoreModel for both strands
+     std::vector<EventRangeForBase> event_maps_1d[NUM_STRANDS];
+@@ -139,7 +139,7 @@
+         }
+ 
+         // Load the events for this strand
+-        std::vector<fast5::Event_Entry> f5_events = f_p->get_basecall_events(event_group, si);
++        std::vector<fast5::Event_Entry> f5_events = f_p->get_basecall_events(si, event_group);
+ 
+         // copy events
+         events[si].resize(f5_events.size());
+@@ -161,7 +161,7 @@
+         // or discarded if this is a 2D read
+ 
+         // NB we use event_group in this call rather than basecall_group as we want the 1D basecalls that match the events
+-        read_sequences_1d[si] = f_p->get_basecall_seq(event_group, si == 0 ? SRT_TEMPLATE : SRT_COMPLEMENT);
++        read_sequences_1d[si] = f_p->get_basecall_seq(si == 0 ? SRT_TEMPLATE : SRT_COMPLEMENT, event_group);
+         event_maps_1d[si] = build_event_map_1d(f_p, read_sequences_1d[si], si, f5_events);
+         std::vector<EventAlignment> alignment =
+             get_eventalignment_for_1d_basecalls(read_sequences_1d[si], event_maps_1d[si], 5, si);
diff --git a/debian/patches/series b/debian/patches/series
index 8d81768..d66d531 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ external-libs.patch
 add-shebang-to-script.patch
 fix-ftbfs-with-gcc6.patch
 reproducible.patch
+fast5-0.5.6.patch

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