diff options
| author | Justin Bedo <cu@cua0.org> | 2022-05-18 08:51:55 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2022-06-19 08:27:00 +1000 |
| commit | f5d976e267ba18d4b5758fb0c9cfdca0f4a203f0 (patch) | |
| tree | 3891aef7483d4cbce9d69d2ced2609a42f067554 | |
| parent | 3ed16534d97e4633a63074f929597d76daaab5ca (diff) | |
quip: fix storing mates
| -rw-r--r-- | tools/quip-app.nix | 1 | ||||
| -rw-r--r-- | tools/quip.patch | 25 |
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; + |