From f5d976e267ba18d4b5758fb0c9cfdca0f4a203f0 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 May 2022 08:51:55 +1000
Subject: quip: fix storing mates

---
 tools/quip-app.nix |  1 +
 tools/quip.patch   | 25 +++++++++++++++++++++++++
 2 files changed, 26 insertions(+)
 create mode 100644 tools/quip.patch

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;
+ 
-- 
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