aboutsummaryrefslogtreecommitdiff
path: root/tools
diff options
context:
space:
mode:
Diffstat (limited to 'tools')
-rw-r--r--tools/quip-app.nix1
-rw-r--r--tools/quip.patch25
2 files changed, 26 insertions, 0 deletions
diff --git a/tools/quip-app.nix b/tools/quip-app.nix
index 422b603..5b380f1 100644
--- a/tools/quip-app.nix
+++ b/tools/quip-app.nix
@@ -16,4 +16,5 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [autoreconfHook];
buildInputs = [zlib];
+ patches = [ ./quip.patch ];
}
diff --git a/tools/quip.patch b/tools/quip.patch
new file mode 100644
index 0000000..6d15057
--- /dev/null
+++ b/tools/quip.patch
@@ -0,0 +1,25 @@
+diff --git a/src/samfmt.c b/src/samfmt.c
+index 043ff7c..38bc217 100644
+--- a/src/samfmt.c
++++ b/src/samfmt.c
+@@ -413,16 +413,10 @@ short_read_t* quip_sam_read(quip_sam_in_t* in)
+ else in->r.seqname.n = 0;
+
+ if (in->f->header && in->b->core.mtid >= 0) {
+- if (in->b->core.mtid == in->b->core.tid) {
+- in->r.mate_seqname.n = 0;
+- str_append_cstr(&in->r.mate_seqname, "=");
+- }
+- else {
+- str_copy_cstr(
+- &in->r.mate_seqname,
+- in->f->header->target_name[in->b->core.mtid],
+- strlen(in->f->header->target_name[in->b->core.mtid]));
+- }
++ str_copy_cstr(
++ &in->r.mate_seqname,
++ in->f->header->target_name[in->b->core.mtid],
++ strlen(in->f->header->target_name[in->b->core.mtid]));
+ }
+ else in->r.mate_seqname.n = 0;
+