diff --git a/README.md b/README.md index f9c2be9..0d02a7c 100644 --- a/README.md +++ b/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` diff --git a/setup.py b/setup.py index cd07472..61687ad 100644 --- a/setup.py +++ b/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', diff --git a/svtyper/classic.py b/svtyper/classic.py index b2e53e4..76dc97c 100755 --- a/svtyper/classic.py +++ b/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') diff --git a/svtyper/singlesample.py b/svtyper/singlesample.py index 71bf3d8..4acb845 100644 --- a/svtyper/singlesample.py +++ b/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) diff --git a/svtyper/version.py b/svtyper/version.py index 9eb4f5f..3e98833 100644 --- a/svtyper/version.py +++ b/svtyper/version.py @@ -1,2 +1,2 @@ __author__ = "Colby Chiang (colbychiang@wustl.edu)" -__version__ = "v0.6.2" +__version__ = "v0.7.0"