Merge pull request #12 from betteridiot/joss-paper

JoSS review fixes
betteridiot · Aug 8, 2018 · fbd5e89 · fbd5e89
2 parents a4043c5 + dde1507
commit fbd5e89
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Showing 6 changed files with 9 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -74,7 +74,7 @@ Bamnostic is meant to be a reduced drop-in replacement for [pysam](https://githu
 Bamnostic comes with an example BAM (and respective BAI) file just to play around with the output. Note, however, that the example BAM file does not contain many reference contigs. Therefore, random access is limited. This example file is made availble through `bamnostic.example_bam`, which is a just a string path to the BAM file within the package.
 
 ```python
->>> bam = bs.AlignmentFile(bs.example_path, 'rb')
+>>> bam = bs.AlignmentFile(bs.example_bam, 'rb')
 ``` 
 
 ### Get the header

diff --git a/README.rst b/README.rst
@@ -93,7 +93,7 @@ within the package.
 
 .. code:: python
 
-    >>> bam = bs.AlignmentFile(bs.example_path, 'rb')
+    >>> bam = bs.AlignmentFile(bs.example_bam, 'rb')
 
 Get the header
 ~~~~~~~~~~~~~~

diff --git a/bamnostic/bgzf.py b/bamnostic/bgzf.py
@@ -945,7 +945,10 @@ def fetch(self, contig=None, start=None, stop=None, region=None,
             if self.ref2tid[query.contig] != tid:
                 raise ValueError('tid and contig name do not match')
         elif query.contig is not None and query.tid is None:
-            query.tid = self.ref2tid[query.contig]
+            try:
+                query.tid = self.ref2tid[query.contig]
+            except KeyError:
+                raise KeyError('{} was not found in the file header'.format(query.contig))
 
         try:
             if query.start > self._header.refs[query.tid][1]:

diff --git a/codemeta.json b/codemeta.json
@@ -37,7 +37,7 @@
   "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": "v0.8.9",
+  "softwareVersion": "v0.8.10",
   "version": "v0.8.2",
   "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md",

diff --git a/docs/paper/codemeta.json b/docs/paper/codemeta.json
@@ -37,7 +37,7 @@
   "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": "v0.8.9",
+  "softwareVersion": "v0.8.10",
   "version": "v0.8.2",
   "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md",

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@ def readme():
 
 setup(
     name='bamnostic',
-    version='0.8.9',
+    version='0.8.10',
     description='Pure Python, OS-agnostic Binary Alignment Map (BAM) random access and parsing tool',
     long_description=readme(),
     url='https://github.com/betteridiot/bamnostic/',