Update parser

Kuanhao-Chao · Sep 9, 2023 · 5724860 · 5724860
1 parent b0ab95a
commit 5724860
Show file tree

Hide file tree

Showing 6 changed files with 11 additions and 7 deletions.
diff --git a/README.md b/README.md
@@ -1,6 +1,5 @@
-
 <p align="center">
-  <img src="./logo.png" alt="Italian Trulli" style="width:85%">
+  <img src="https://storage.googleapis.com/storage.khchao.com/figures/Splam/logo.png" alt="Italian Trulli" style="width:85%">
 </p>
 
 

diff --git a/src/include/htslib b/src/include/htslib
diff --git a/src/setup.py b/src/setup.py
@@ -7,7 +7,7 @@
 from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
 
-VERSION = "1.0.3"
+VERSION = "1.0.7"
 
 # Convert distutils Windows platform specifiers to CMake -A arguments
 PLAT_TO_CMAKE = {
@@ -17,6 +17,8 @@
     "win-arm64": "ARM64",
 }
 
+this_directory = Path(__file__).resolve().parent
+long_description = (this_directory / "../README.md").read_text()
 
 # A CMakeExtension needs a sourcedir instead of a file list.
 # The name must be the _single_ output extension from the CMake build.
@@ -142,4 +144,6 @@ def build_extension(self, ext: CMakeExtension) -> None:
     cmdclass={"build_ext": CMakeBuild},
     extras_require={"test": "pytest"},
 	entry_points={'console_scripts': ['splam = splam.main:main'], },
+    long_description=long_description,
+    long_description_content_type='text/markdown'
 )
diff --git a/src/splam/__init__.py b/src/splam/__init__.py
@@ -1 +1 @@
-__version__ = '1.0.2'
+__version__ = '1.0.7'
diff --git a/src/splam/header.py b/src/splam/header.py
@@ -8,4 +8,4 @@
 __license__ = "MIT"
 __maintainer__ = "developer"
 __status__ = "Kuan-Hao Chao"
-__version__ = "1.0.3"
+__version__ = "1.0.7"
diff --git a/src/splam/parse.py b/src/splam/parse.py
@@ -86,7 +86,8 @@ def create_donor_acceptor_bed(junction_bed, junction_dir, reference_genome):
                 acceptor_s = acceptor - config.QUARTER_SEQ_LEN
                 acceptor_e = acceptor + flanking_size
 
-
+            if chr not in chrs.keys():
+                continue
             if donor_e >= chrs[chr] or acceptor_e >= chrs[chr]:
                 continue
             if donor_s < 0 or acceptor_s < 0:
+6 −5		Makefile
+23 −3		bgzf.c
+10 −1		cram/cram_codecs.c
+26 −1		cram/cram_io.c
+35 −0		fuzz_settings.h
+60 −9		header.c
+10 −2		hfile.c
+17 −0		hts.c
+5 −10		htsfile.c
+4 −0		htslib/hfile.h
+1 −1		htslib/hts_endian.h
+9 −3		htslib/sam.h
+52 −33		htslib/vcf.h
+11 −2		kstring.c
+61 −9		sam.c
+1 −0		test/sam_filter/filter.tst
+1 −0		test/sam_filter/func8.out
+6 −0		test/test_view.c
+485 −155		vcf.c