update 0.2.13

parklab · Sep 15, 2020 · d6ab56a · d6ab56a
1 parent f038ca8
commit d6ab56a
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Showing 21 changed files with 51 additions and 13 deletions.
diff --git a/docs/version_history.rst b/docs/version_history.rst
@@ -3,6 +3,9 @@ Version History
 
 v0.2.x release series
 ---------------------
+0.2.13 (2020.09.13):
+	- adjust target line for deletion in VCF
+
 0.2.12 (2020.09.15):
 	- adjust target line for deletion in VCF
 

diff --git a/pack.sh b/pack.sh
@@ -2,5 +2,5 @@ pip uninstall -y bamsnap
 rm -rf build
 rm -rf ./dist/*
 python3 setup.py sdist bdist_wheel
-pip install ./dist/bamsnap-0.2.12-py3-none-any.whl
+pip install ./dist/bamsnap-0.2.13-py3-none-any.whl
 # twine upload dist/*
diff --git a/setup.py b/setup.py
@@ -20,7 +20,7 @@
 }
 
 setup(name='bamsnap',
-      version='0.2.12',
+      version='0.2.13',
       url='https://github.com/danielmsk/bamsnap',
       license='MIT',
       author='Daniel Minseok Kwon',

diff --git a/src/bamsnap.egg-info/PKG-INFO b/src/bamsnap.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bamsnap
-Version: 0.2.12
+Version: 0.2.13
 Summary: A converter from .bam to .png for specific genomic region.
 Home-page: https://github.com/danielmsk/bamsnap
 Author: Daniel Minseok Kwon

diff --git a/src/bamsnap/__pycache__/_options.cpython-37.pyc b/src/bamsnap/__pycache__/_options.cpython-37.pyc
diff --git a/src/bamsnap/__pycache__/bamsnap.cpython-37.pyc b/src/bamsnap/__pycache__/bamsnap.cpython-37.pyc
diff --git a/src/bamsnap/_options.py b/src/bamsnap/_options.py
@@ -98,15 +98,15 @@ def set_pos_list(opt):
                     p1['t_spos'] = int(arr[1])
                     p1['t_epos'] = int(arr[1]) + 1
                 elif len(ref) > len(alt):
-                    p1['t_spos'] = int(arr[1])
-                    p1['t_epos'] = int(arr[1]) + len(ref) + 1
+                    p1['t_spos'] = int(arr[1]) + 1
+                    p1['t_epos'] = int(arr[1]) + len(ref) 
                 elif len(ref) < len(alt):
-                    p1['t_spos'] = int(arr[1])
-                    p1['t_epos'] = int(arr[1]) + len(alt) + 1
+                    p1['t_spos'] = int(arr[1]) + 1
+                    p1['t_epos'] = int(arr[1]) + len(alt) 
                 else:
-                    p1['t_spos'] = int(arr[1])
-                    p1['t_epos'] = int(arr[1]) + len(alt) + 1
-                    
+                    p1['t_spos'] = int(arr[1]) + 1
+                    p1['t_epos'] = int(arr[1]) + len(alt)
+
                 p1['g_spos'] = p1['t_spos'] - int(opt['margin'])
                 p1['g_epos'] = p1['t_epos'] + int(opt['margin'])
                 poslist.append(p1)

diff --git a/src/bamsnap/data/conf.json b/src/bamsnap/data/conf.json
@@ -1,6 +1,6 @@
 {
     "TITLE":"BAMSNAP",
-    "VERSION":"0.2.12",
+    "VERSION":"0.2.13",
     "VERSION_DATE":"2020-09-15",
     "PROG":"bamsnap",
     "options":[

diff --git a/tests/data/test_DEL_chr12_47977510.vcf b/tests/data/test_DEL_chr12_47977510.vcf
@@ -0,0 +1 @@
+chr12	47977510	.	CTTGTTCCAACCTGCCACCCCCAGCTGACCTGTCAGGCCCGAGGCAATGTCCTCCCCAACCCACTGCACACACAGACACCAGACACTCA	C
diff --git a/tests/data/test_DEL_chr12_47977510_F.bam b/tests/data/test_DEL_chr12_47977510_F.bam
diff --git a/tests/data/test_DEL_chr12_47977510_F.bam.bai b/tests/data/test_DEL_chr12_47977510_F.bam.bai
diff --git a/tests/data/test_DEL_chr12_47977510_M.bam b/tests/data/test_DEL_chr12_47977510_M.bam
diff --git a/tests/data/test_DEL_chr12_47977510_M.bam.bai b/tests/data/test_DEL_chr12_47977510_M.bam.bai
diff --git a/tests/data/test_DEL_chr12_47977510_P.bam b/tests/data/test_DEL_chr12_47977510_P.bam
diff --git a/tests/data/test_DEL_chr12_47977510_P.bam.bai b/tests/data/test_DEL_chr12_47977510_P.bam.bai
diff --git a/tests/out/test_DEL_2.png b/tests/out/test_DEL_2.png
diff --git a/tests/out/test_DEL_chr12.png b/tests/out/test_DEL_chr12.png
diff --git a/tests/out/test_DEL_chr12_1.png b/tests/out/test_DEL_chr12_1.png
diff --git a/tests/out/test_DEL_chr12_2.png b/tests/out/test_DEL_chr12_2.png
diff --git a/tests/out/test_DEL_chr12_3.png b/tests/out/test_DEL_chr12_3.png
diff --git a/tests/test_run.py b/tests/test_run.py
@@ -250,7 +250,7 @@
     -save_image_only
 """)  # coordinates track example 3
 
-#180097878-180098507
+
 cmdlist.append("""
     -bam ./data/test_DEL_4_180097876_180097877.bam \
     -vcf ./data/test_DEL_4.vcf \
@@ -263,6 +263,41 @@
     -save_image_only
 """)  # coordinates track example 3
 
+cmdlist.append("""
+    -bam ./data/test_DEL_chr12_47977510_F.bam ./data/test_DEL_chr12_47977510_M.bam ./data/test_DEL_chr12_47977510_P.bam \
+    -vcf ./data/test_DEL_chr12_47977510.vcf \
+    -margin 20 \
+    -title "F" "M" "P" \
+    -out ./out/test_DEL_chr12_1.png \
+    -show_soft_clipped \
+    -read_color_by interchrom \
+    -read_group strand \
+    -save_image_only
+""")  
+
+cmdlist.append("""
+    -bam ./data/test_DEL_chr12_47977510_F.bam ./data/test_DEL_chr12_47977510_M.bam ./data/test_DEL_chr12_47977510_P.bam \
+    -vcf ./data/test_DEL_chr12_47977510.vcf \
+    -margin 1000 \
+    -title "F" "M" "P" \
+    -out ./out/test_DEL_chr12_2.png \
+    -show_soft_clipped \
+    -read_color_by interchrom \
+    -read_group strand \
+    -save_image_only
+""")  
+
+cmdlist.append("""
+    -bam ./data/test_DEL_chr12_47977510_F.bam ./data/test_DEL_chr12_47977510_M.bam ./data/test_DEL_chr12_47977510_P.bam \
+    -vcf ./data/test_DEL_chr12_47977510.vcf \
+    -margin 5000 \
+    -title "F" "M" "P" \
+    -out ./out/test_DEL_chr12_3.png \
+    -show_soft_clipped \
+    -read_color_by interchrom \
+    -read_group strand \
+    -save_image_only
+""")
 
 cmdlist.append("""
     -bam ./data/test_noMDtag_1_102345_103355.bam \
@@ -286,7 +321,6 @@
 """)
 
 
-
 def test_run():
     for cmd in cmdlist:
         # cmd = cmdlist[-1]
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		chr12 47977510 . CTTGTTCCAACCTGCCACCCCCAGCTGACCTGTCAGGCCCGAGGCAATGTCCTCCCCAACCCACTGCACACACAGACACCAGACACTCA C