[med-svn] [ariba] 01/01: Adapt to fermi-lite which does not conflict with bwa

[Andreas Tille]

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tille pushed a commit to branch master
in repository ariba.

commit 92be90993f020d5d2395f083a42a48cebd5bab49
Author: Andreas Tille <tille at debian.org>
Date:   Sat Feb 4 12:26:37 2017 +0100

    Adapt to fermi-lite which does not conflict with bwa
---
 debian/patches/series                              |  1 +
 debian/patches/use_bwa_compatible_fermi-lite.patch | 30 ++++++++++++++++++++++
 2 files changed, 31 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 0ec39a7..99a6b20 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 use_debian_packaged_libs_for_extension.patch
+# use_bwa_compatible_fermi-lite.patch
diff --git a/debian/patches/use_bwa_compatible_fermi-lite.patch b/debian/patches/use_bwa_compatible_fermi-lite.patch
new file mode 100644
index 0000000..7ebc94d
--- /dev/null
+++ b/debian/patches/use_bwa_compatible_fermi-lite.patch
@@ -0,0 +1,30 @@
+Description: Adapt to fermi-lite which does not conflict with bwa
+  An issue on fermi-lite upstream tracker
+    https://github.com/lh3/fermi-lite/issues/5
+  suggests to take over a patch for the Debian package which would
+  enable making it co-usable with libbwa-dev (which is needed in
+  libseqlib).  This patch adapts ariba to the potential change in
+  fermi-lite.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 04 Feb 2017 09:09:26 +0100
+
+--- a/ariba/ext/fml-asm_ariba.cpp
++++ b/ariba/ext/fml-asm_ariba.cpp
+@@ -136,7 +136,7 @@ int assemble(char *readsFile, char *fast
+ {
+     fml_opt_t opt;
+     int n_seqs, n_utg;
+-    bseq1_t *seqs;
++    fml_seq1_t *seqs;
+     fml_opt_init(&opt);
+     opt.max_cnt = 10000;
+     opt.mag_opt.flag |= MAG_F_AGGRESSIVE;
+@@ -176,7 +176,7 @@ int assemble(char *readsFile, char *fast
+ 
+             // need to get the reads from the file every time, instead of before
+             // the loop because fml_assemble() destroys them :(
+-            seqs = bseq_read(readsFile, &n_seqs);
++            seqs = fml_seq_read(readsFile, &n_seqs);
+             if (seqs && n_seqs > 0) {
+                 fml_utg_t *utg;
+                 utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);

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