Merge pull request #97 from hall-lab/v0.7.0

v0.7.0

README.md

@@ -20,7 +20,7 @@ Requirements:
 
     pip install git+https://github.com/hall-lab/svtyper.git
 
-`svtyper` depends on [pysam][0] _(version 0.12.0 or newer)_, [numpy][1], and [scipy][2]; `svtyper-sso` additionally depends on [cytoolz][7]. If the dependencies aren't already available on your system, `pip` will attempt to download and install them.
+`svtyper` depends on [pysam][0] _(version 0.15.0 or newer)_, [numpy][1], and [scipy][2]; `svtyper-sso` additionally depends on [cytoolz][7]. If the dependencies aren't already available on your system, `pip` will attempt to download and install them.
 
 ## `svtyper` vs `svtyper-sso`
 

setup.py

@@ -23,7 +23,7 @@
     setup_requires=['pytest-runner'],
     tests_require=['pytest'],
     install_requires=[
-        'pysam>=0.12.0',
+        'pysam>=0.15.0',
         'numpy',
         'scipy',
         'cytoolz>=0.8.2',

svtyper/classic.py

@@ -32,7 +32,7 @@ def get_args():
     parser.add_argument('-n', dest='num_samp', metavar='INT', type=int, required=False, default=1000000, help='number of reads to sample from BAM file for building insert size distribution [1000000]')
     parser.add_argument('-q', '--sum_quals', action='store_true', required=False, help='add genotyping quality to existing QUAL (default: overwrite QUAL field)')
     parser.add_argument('--max_reads', metavar='INT', type=int, default=None, required=False, help='maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: unlimited)')
-    parser.add_argument('--max_ci_dist', metavar='INT', type=int, default=1e10, required=False, help='maximum size of a confidence interval before 95% CI is used intead (default: 1e10)')
+    parser.add_argument('--max_ci_dist', metavar='INT', type=int, default=1e10, required=False, help='maximum size of a confidence interval before 95%% CI is used intead (default: 1e10)')
     parser.add_argument('--split_weight', metavar='FLOAT', type=float, required=False, default=1, help='weight for split reads [1]')
     parser.add_argument('--disc_weight', metavar='FLOAT', type=float, required=False, default=1, help='weight for discordant paired-end reads [1]')
     parser.add_argument('-w', '--write_alignment', metavar='FILE', dest='alignment_outpath', type=str, required=False, default=None, help='write relevant reads to BAM file')

svtyper/singlesample.py

@@ -28,7 +28,7 @@ def get_args():
     parser.add_argument('-n', dest='num_samp', metavar='INT', type=int, required=False, default=1000000, help='number of reads to sample from BAM file for building insert size distribution [1000000]')
     parser.add_argument('-q', '--sum_quals', action='store_true', required=False, help='add genotyping quality to existing QUAL (default: overwrite QUAL field)')
     parser.add_argument('--max_reads', metavar='INT', type=int, default=1000, required=False, help='maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: 1000)')
-    parser.add_argument('--max_ci_dist', metavar='INT', type=int, default=1e10, required=False, help='maximum size of a confidence interval before 95% CI is used intead (default: 1e10)')
+    parser.add_argument('--max_ci_dist', metavar='INT', type=int, default=1e10, required=False, help='maximum size of a confidence interval before 95%% CI is used intead (default: 1e10)')
     parser.add_argument('--split_weight', metavar='FLOAT', type=float, required=False, default=1, help='weight for split reads [1]')
     parser.add_argument('--disc_weight', metavar='FLOAT', type=float, required=False, default=1, help='weight for discordant paired-end reads [1]')
     parser.add_argument('--debug', action='store_true', help=argparse.SUPPRESS)

svtyper/version.py

@@ -1,2 +1,2 @@
 __author__ = "Colby Chiang ([email protected])"
-__version__ = "v0.6.2"
+__version__ = "v0.7.0"