[med-svn] [nanopolish] 07/08: Fix compatibility with fast5 0.5.6
Afif Elghraoui
afif at moszumanska.debian.org
Fri Aug 12 07:08:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
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
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/nanopolish.git
More information about the debian-med-commit
mailing list