Fix encoding process for ‘B, S’ type option in alignment.

chrovis · Sep 5, 2022 · 95fdd56 · 95fdd56
1 parent c7cd8c4
commit 95fdd56
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Showing 5 changed files with 15 additions and 3 deletions.
diff --git a/src/cljam/io/bam/encoder.clj b/src/cljam/io/bam/encoder.clj
@@ -66,7 +66,7 @@
                 (lsb/write-bytes writer (byte-array 1 (byte \S)))
                 (lsb/write-int writer (count array))
                 (doseq [v array]
-                  (lsb/write-short writer (Short/parseShort v))))
+                  (lsb/write-ushort writer (Integer/parseInt v))))
            \i nil
            \I nil
            \f nil))))

diff --git a/test-resources/bam/include-BS-type-option.bam b/test-resources/bam/include-BS-type-option.bam
diff --git a/test-resources/sam/include-BS-type-option.sam b/test-resources/sam/include-BS-type-option.sam
@@ -0,0 +1,3 @@
+@SQ	SN:ref	LN:45
+q001	0	ref	10	60	16M	*	0	0	AAAAGGGGTTTTCCCC	*	Xa:A:p	Xi:i:-100	Xf:f:-1.4e3	Xz:Z:AATTGGCC
+q006	0	ref	10	60	16M	*	0	0	AAAAGGGGTTTTCCCC	*	XS:B:S,0,32767,32768,65535
diff --git a/test/cljam/io/sam_test.clj b/test/cljam/io/sam_test.clj
@@ -34,6 +34,8 @@
               opts-sam-file
               seq-asterisk-sam-file
               seq-asterisk-bam-file
+              include-BS-type-option-sam-file
+              include-BS-type-option-bam-file
               opts-bam-file
               test-sam-blocks
               test-bai-file
@@ -298,7 +300,8 @@
                  (is (= (seq alignments)
                         (seq (sam/read-alignments bam-rdr)))))))))
     test-sam-file
-    seq-asterisk-sam-file))
+    seq-asterisk-sam-file
+    include-BS-type-option-sam-file))
 
 (deftest bam->sam-convert-test
   (are [target-bam]
@@ -316,7 +319,8 @@
                  (is (= (seq alignments)
                         (seq (sam/read-alignments sam-rdr)))))))))
     test-bam-file
-    seq-asterisk-bam-file))
+    seq-asterisk-bam-file
+    include-BS-type-option-bam-file))
 
 (deftest sam-writer-test
   (with-before-after {:before (prepare-cache!)

diff --git a/test/cljam/test_common.clj b/test/cljam/test_common.clj
@@ -131,6 +131,9 @@
 (def opts-sam-file "test-resources/sam/opts.sam")
 
 (def seq-asterisk-sam-file "test-resources/sam/seq-asterisk.sam")
+
+(def include-BS-type-option-sam-file "test-resources/sam/include-BS-type-option.sam")
+
 ;; ### BAM files
 
 (def test-bam-file "test-resources/bam/test.bam")
@@ -148,6 +151,8 @@
 (def normalize-after-bam-file "test-resources/bam/normalize_after.bam")
 (def opts-bam-file "test-resources/bam/opts.bam")
 
+(def include-BS-type-option-bam-file "test-resources/bam/include-BS-type-option.bam")
+
 ;; ### BAM index files
 
 (def test-bai-file "test-resources/bam/test.sorted.bam.bai")