From dde2b46c5910c7932927c6e8ab328ef3a23b3c0c Mon Sep 17 00:00:00 2001
From: Haibao Tang <tanghaibao@gmail.com>
Date: Wed, 24 Jul 2024 20:34:46 +0800
Subject: [PATCH] test both w/ seqids and wo/ seqids

---
 .../references/test.resolution_500000.json    |   10 +-
 .../test.resolution_500000.seqids.json        | 3015 +++++++++++++++++
 tests/assembly/hic.py/tests.yml               |    9 +-
 3 files changed, 3030 insertions(+), 4 deletions(-)
 create mode 100644 tests/assembly/hic.py/references/test.resolution_500000.seqids.json

diff --git a/tests/assembly/hic.py/references/test.resolution_500000.json b/tests/assembly/hic.py/references/test.resolution_500000.json
index b33346a3..039e8fa7 100644
--- a/tests/assembly/hic.py/references/test.resolution_500000.json
+++ b/tests/assembly/hic.py/references/test.resolution_500000.json
@@ -3004,12 +3004,16 @@
     ],
     "resolution": 500000,
     "sizes": {
+        "An_chr4": 38,
         "Cv_chr4": 37,
+        "Ky_chr4": 38,
         "Le_chr4": 39
     },
     "starts": {
-        "Cv_chr4": 0,
-        "Le_chr4": 37
+        "An_chr4": 0,
+        "Cv_chr4": 38,
+        "Ky_chr4": 75,
+        "Le_chr4": 113
     },
-    "total_bins": 76
+    "total_bins": 152
 }
\ No newline at end of file
diff --git a/tests/assembly/hic.py/references/test.resolution_500000.seqids.json b/tests/assembly/hic.py/references/test.resolution_500000.seqids.json
new file mode 100644
index 00000000..b33346a3
--- /dev/null
+++ b/tests/assembly/hic.py/references/test.resolution_500000.seqids.json
@@ -0,0 +1,3015 @@
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+    ],
+    "resolution": 500000,
+    "sizes": {
+        "Cv_chr4": 37,
+        "Le_chr4": 39
+    },
+    "starts": {
+        "Cv_chr4": 0,
+        "Le_chr4": 37
+    },
+    "total_bins": 76
+}
\ No newline at end of file
diff --git a/tests/assembly/hic.py/tests.yml b/tests/assembly/hic.py/tests.yml
index bceb604d..3c6a3448 100644
--- a/tests/assembly/hic.py/tests.yml
+++ b/tests/assembly/hic.py/tests.yml
@@ -1,6 +1,13 @@
 bam2mat:
   action: bam2mat
-  opts: --seqids=__DIR__/inputs/seqids
+  opts:
+  args: __DIR__/inputs/test.bam
+  outputs: [__DIR__/inputs/test.resolution_500000.json]
+  references: [references/test.resolution_500000.json]
+
+bam2mat_seqids:
+  action: bam2mat
+  opts: __DIR__/inputs/seqids
   args: __DIR__/inputs/test.bam
   outputs: [__DIR__/inputs/test.resolution_500000.json]
   references: [references/test.resolution_500000.json]
\ No newline at end of file