Fixes #25: corrected regression error caused by recent bug fix

betteridiot · Nov 5, 2018 · 843687b · 843687b
1 parent 930f972
commit 843687b
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Showing 5 changed files with 11 additions and 11 deletions.
diff --git a/bamnostic/bam.py b/bamnostic/bam.py
@@ -591,14 +591,14 @@ def fetch(self, contig=None, start=None, stop=None, region=None,
                 # check to see if the read is out of bounds of the region
                 # On the wrong contig -> not the right place
                 if next_read.reference_name != query.contig: 
-                    return None
+                    return
 
                 # Read is too far left -> keep going
                 elif (next_read.pos + len(next_read.seq)) < query.start:
                     continue
 
                 # Originates outside, but overlaps
-                elif next_read.pos < query.start <= (next_read.pos + len(next_read)):
+                elif next_read.pos < query.start <= (next_read.pos + len(next_read.seq)):
                     yield next_read
 
                 # Read wholly inside region
@@ -607,15 +607,15 @@ def fetch(self, contig=None, start=None, stop=None, region=None,
 
                 # Read too far right -> gotta stop
                 elif query.stop <= next_read.pos:
-                    return None
+                    return
 
                 # check for stop iteration
                 elif next_read:
                     yield next_read
 
                 # Empty read
                 else:
-                    return None
+                    return
 
             # Read until the end of file
             else: 

diff --git 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": "v1.0.2,
-  "version": "v1.0.2",
+  "softwareVersion": "v1.0.3,
+  "version": "v1.0.3",
   "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/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": "v1.0.2",
-  "version": "v1.0.2",
+  "softwareVersion": "v1.0.3",
+  "version": "v1.0.3",
   "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
@@ -24,9 +24,9 @@
 author = 'Marcus D. Sherman'
 
 # The short X.Y version
-version = '1.0.2'
+version = '1.0.3'
 # The full version, including alpha/beta/rc tags
-release = '1.0.2'
+release = '1.0.3'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/setup.py b/setup.py
@@ -29,7 +29,7 @@ def readme():
 
 setup(
     name='bamnostic',
-    version='1.0.2',
+    version='1.0.3',
     description='Pure Python, OS-agnostic Binary Alignment Map (BAM) random access and parsing tool',
     long_description=readme(),
     url='https://github.com/betteridiot/bamnostic/',