diff --git a/bamnostic/utils.py b/bamnostic/utils.py index f33ef44..2d75da3 100644 --- a/bamnostic/utils.py +++ b/bamnostic/utils.py @@ -388,7 +388,7 @@ def unpack(fmt, _io): try: # if it is byte object out = struct.unpack(fmt, _io) - except TypeError: + except: # if it is a file object out = struct.unpack(fmt, _io.read(size)) if len(out) > 1: diff --git a/codemeta.json b/codemeta.json index 4c9ce40..3d67a3e 100644 --- a/codemeta.json +++ b/codemeta.json @@ -37,8 +37,8 @@ "description": "BAMnostic is a Pure Python OS, version, and runtime agnostic BAM file parser", "keywords": "BAM, pysam, genomics, genetics, htslib, samtools", "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE", - "softwareVersion": "v1.0.6, - "version": "v1.0.6", + "softwareVersion": "v1.0.7, + "version": "v1.0.7", "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md", "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md", "issueTracker": "https://github.com/betteridiot/bamnostic/issues", diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle index b49e423..2230d0f 100644 Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo index c31f48c..a660ccd 100644 --- a/docs/build/html/.buildinfo +++ b/docs/build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: bcdbf5372f05aa74274336aa5687ab30 +config: 6d491e59de0287a809983c89c4c65de7 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/_modules/bamnostic/bai.html b/docs/build/html/_modules/bamnostic/bai.html index b19ca74..caff978 100644 --- a/docs/build/html/_modules/bamnostic/bai.html +++ b/docs/build/html/_modules/bamnostic/bai.html @@ -8,7 +8,7 @@ - bamnostic.bai — bamnostic 1.0.6 documentation + bamnostic.bai — bamnostic 1.0.7 documentation @@ -56,7 +56,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/_modules/bamnostic/bgzf.html b/docs/build/html/_modules/bamnostic/bgzf.html index 749096e..256d70e 100644 --- a/docs/build/html/_modules/bamnostic/bgzf.html +++ b/docs/build/html/_modules/bamnostic/bgzf.html @@ -8,7 +8,7 @@ - bamnostic.bgzf — bamnostic 1.0.6 documentation + bamnostic.bgzf — bamnostic 1.0.7 documentation @@ -56,7 +56,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/_modules/bamnostic/core.html b/docs/build/html/_modules/bamnostic/core.html index 7b5e62d..ea5fdf1 100644 --- a/docs/build/html/_modules/bamnostic/core.html +++ b/docs/build/html/_modules/bamnostic/core.html @@ -8,7 +8,7 @@ - bamnostic.core — bamnostic 1.0.6 documentation + bamnostic.core — bamnostic 1.0.7 documentation @@ -56,7 +56,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/_modules/bamnostic/utils.html b/docs/build/html/_modules/bamnostic/utils.html index 0788c64..d7361b7 100644 --- a/docs/build/html/_modules/bamnostic/utils.html +++ b/docs/build/html/_modules/bamnostic/utils.html @@ -8,7 +8,7 @@ - bamnostic.utils — bamnostic 1.0.6 documentation + bamnostic.utils — bamnostic 1.0.7 documentation @@ -56,7 +56,7 @@
- 1.0.6 + 1.0.7
@@ -539,7 +539,7 @@

Source code for bamnostic.utils

     try:
         # if it is byte object
         out = struct.unpack(fmt, _io)
-    except TypeError:
+    except:
         # if it is a file object
         out = struct.unpack(fmt, _io.read(size))
     if len(out) > 1:
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
index 7a89235..a41d20a 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -8,7 +8,7 @@
   
   
   
-  Overview: module code — bamnostic 1.0.6 documentation
+  Overview: module code — bamnostic 1.0.7 documentation
   
 
   
@@ -56,7 +56,7 @@
             
             
               
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js index 117e2ba..156426d 100644 --- a/docs/build/html/_static/documentation_options.js +++ b/docs/build/html/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.0.6', + VERSION: '1.0.7', LANGUAGE: 'en', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/build/html/bamnostic.html b/docs/build/html/bamnostic.html index bd09ef9..6987860 100644 --- a/docs/build/html/bamnostic.html +++ b/docs/build/html/bamnostic.html @@ -8,7 +8,7 @@ - bamnostic package — bamnostic 1.0.6 documentation + bamnostic package — bamnostic 1.0.7 documentation @@ -58,7 +58,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html index 21cd34c..8d2e09e 100644 --- a/docs/build/html/genindex.html +++ b/docs/build/html/genindex.html @@ -9,7 +9,7 @@ - Index — bamnostic 1.0.6 documentation + Index — bamnostic 1.0.7 documentation @@ -57,7 +57,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/index.html b/docs/build/html/index.html index 544d8ea..8392c90 100644 --- a/docs/build/html/index.html +++ b/docs/build/html/index.html @@ -8,7 +8,7 @@ - Welcome to bamnostic’s documentation! — bamnostic 1.0.6 documentation + Welcome to bamnostic’s documentation! — bamnostic 1.0.7 documentation @@ -57,7 +57,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/install.html b/docs/build/html/install.html index 8620219..13abd82 100644 --- a/docs/build/html/install.html +++ b/docs/build/html/install.html @@ -8,7 +8,7 @@ - Installation — bamnostic 1.0.6 documentation + Installation — bamnostic 1.0.7 documentation @@ -58,7 +58,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv index 75c51f3..888ede8 100644 Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html index b6f1547..3dac50c 100644 --- a/docs/build/html/py-modindex.html +++ b/docs/build/html/py-modindex.html @@ -8,7 +8,7 @@ - Python Module Index — bamnostic 1.0.6 documentation + Python Module Index — bamnostic 1.0.7 documentation @@ -59,7 +59,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/quickstart.html b/docs/build/html/quickstart.html index e4567d9..89a4e3f 100644 --- a/docs/build/html/quickstart.html +++ b/docs/build/html/quickstart.html @@ -8,7 +8,7 @@ - Quickstart — bamnostic 1.0.6 documentation + Quickstart — bamnostic 1.0.7 documentation @@ -58,7 +58,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/search.html b/docs/build/html/search.html index eb77388..4903309 100644 --- a/docs/build/html/search.html +++ b/docs/build/html/search.html @@ -8,7 +8,7 @@ - Search — bamnostic 1.0.6 documentation + Search — bamnostic 1.0.7 documentation @@ -56,7 +56,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/build/html/support.html b/docs/build/html/support.html index 7caff62..a65263e 100644 --- a/docs/build/html/support.html +++ b/docs/build/html/support.html @@ -8,7 +8,7 @@ - Citation and Support — bamnostic 1.0.6 documentation + Citation and Support — bamnostic 1.0.7 documentation @@ -57,7 +57,7 @@
- 1.0.6 + 1.0.7
diff --git a/docs/paper/codemeta.json b/docs/paper/codemeta.json index ca591e9..154d901 100644 --- a/docs/paper/codemeta.json +++ b/docs/paper/codemeta.json @@ -37,8 +37,8 @@ "description": "BAMnostic: an OS-agnostic toolkit for genomic sequence analysis", "keywords": "BAM, pysam, genomics, genetics, htslib, samtools", "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE", - "softwareVersion": "v1.0.6", - "version": "v1.0.6", + "softwareVersion": "v1.0.7", + "version": "v1.0.7", "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md", "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md", "issueTracker": "https://github.com/betteridiot/bamnostic/issues", diff --git a/docs/source/conf.py b/docs/source/conf.py index ece8d18..0522f7d 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -24,9 +24,9 @@ author = 'Marcus D. Sherman' # The short X.Y version -version = '1.0.6' +version = '1.0.7' # The full version, including alpha/beta/rc tags -release = '1.0.6' +release = '1.0.7' # -- General configuration --------------------------------------------------- diff --git a/setup.py b/setup.py index b9bd5cb..1c6720c 100644 --- a/setup.py +++ b/setup.py @@ -29,7 +29,7 @@ def readme(): setup( name='bamnostic', - version='1.0.6', + version='1.0.7', description='Pure Python, OS-agnostic Binary Alignment Map (BAM) random access and parsing tool', long_description=readme(), url='https://github.com/betteridiot/bamnostic/',