diff --git a/HISTORY.md b/HISTORY.md index 9470af9..0b00f82 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,4 +1,5 @@ -## 1.1.0 (in progress) +## 1.0.1 +- Add support for click 7.0. ## 1.0.0 - Fix for min-length filtering with paired samples. Previously required only one read to be longer, fix requires both. diff --git a/setup.py b/setup.py index f093f39..d0575d6 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ def read(fname): setup( name='umis', - version='1.0.0', + version='1.0.1', description='Package for estimating UMI counts in Transcript Tag Counting data.', packages=find_packages(), install_requires=['click', 'pysam>=0.8.3', 'pandas', 'regex', 'scipy', 'toolz'], diff --git a/umis/umis.py b/umis/umis.py index b2c5a5c..abe131e 100644 --- a/umis/umis.py +++ b/umis/umis.py @@ -24,7 +24,7 @@ import scipy.io, scipy.sparse import click -VERSION = "1.0.0" +VERSION = "1.0.1" logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) @@ -1342,13 +1342,13 @@ def umis(): umis.add_command(fastqtransform) umis.add_command(tagcount) umis.add_command(fasttagcount) -umis.add_command(cb_histogram) -umis.add_command(umi_histogram) -umis.add_command(cb_filter) -umis.add_command(sb_filter) -umis.add_command(mb_filter) -umis.add_command(add_uid) +umis.add_command(cb_histogram, name="cb_histogram") +umis.add_command(umi_histogram, name="umi_histogram") +umis.add_command(cb_filter, name="cb_filter") +umis.add_command(sb_filter, name="sb_filter") +umis.add_command(mb_filter, name="mb_filter") +umis.add_command(add_uid, name="add_uid") umis.add_command(kallisto) umis.add_command(bamtag) -umis.add_command(demultiplex_samples) -umis.add_command(subset_bamfile) +umis.add_command(demultiplex_samples, name="demultiplex_samples") +umis.add_command(subset_bamfile, name="subset_bamfile")