Commit bf7a9aff authored by Hoogenboom, Jerry's avatar Hoogenboom, Jerry

TSSV v2.0.0

  - Removed dependency on external tssv package (it is no longer compatible).
  - Greatly increased performance by deduplicating the input reads.
  - Removed the -q/--is-fastq option in favour of automatic detection.
  - Changed the default value for -m/--mismatches from 0.08 to 0.1.
  - Changed the default value for -n/--indel-score from 1 to 2.
  - Added the -X/--no-deduplicate option to disable deduplication.
  - Fixed potential crash that could occur under very specific circumstances.
parent 670d34f9
......@@ -63,4 +63,30 @@ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*******************************************************************************
TSSV: Targeted characterisation of short structural variation
Copyright (c) 2012-2018 Jeroen F.J. Laros <j.f.j.laros@lumc.nl>
Copyright (c) 2016 Jerry Hoogenboom <j.hoogenboom@nfi.minvenj.nl>
Copyright (c) 2012 Jaap W.F. van der Heijden
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is furnished to do
so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
......@@ -29,8 +29,10 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog
------------------
v1.1.2
v1.2.0
- Includes Pipeline v1.0.4
- Includes Samplevis v2.2.1
- Includes TSSV v2.0.0
v1.1.1
- Includes TSSV v1.1.1
......@@ -356,6 +358,9 @@ v1.0.0
Pipeline
~~~~~~~~
v1.0.4
- Removed reference to the 'is-fastq' option of TSSV.
v1.0.3
- Fixed glitch that caused the 'bgprofiles.html' output file of the
reference-database analysis to lack a proper title.
......@@ -479,6 +484,15 @@ v1.0.0
TSSV
~~~~
v2.0.0
- Removed dependency on external tssv package (it is no longer compatible).
- Greatly increased performance by deduplicating the input reads.
- Removed the -q/--is-fastq option in favour of automatic detection.
- Changed the default value for -m/--mismatches from 0.08 to 0.1.
- Changed the default value for -n/--indel-score from 1 to 2.
- Added the -X/--no-deduplicate option to disable deduplication.
- Fixed potential crash that could occur under very specific circumstances.
v1.1.1
- Fixed incorrect calculation of tLeft, fLeft, rLeft, tRight and fRight
columns in the report output file when -T/--num-threads was set to 2 or
......
......@@ -24,7 +24,7 @@ including tools for characterisation and filtering of PCR stutter artefacts and
other systemic noise, and for automatic detection of the alleles in a sample.
"""
__version_info__ = ('1', '1', '2', 'dev1')
__version_info__ = ('1', '2', '0', 'dev1')
__version__ = '.'.join(__version_info__)
usage = __doc__.split("\n\n\n")
......
#!/usr/bin/env python
#
# Copyright (C) 2017 Jerry Hoogenboom
# Copyright (C) 2019 Jerry Hoogenboom
#
# This file is part of FDSTools, data analysis tools for Next
# Generation Sequencing of forensic DNA markers.
......
This diff is collapsed.
#!/usr/bin/env python
#
# Copyright (C) 2016 Jerry Hoogenboom
# Copyright (C) 2019 Jerry Hoogenboom
#
# This file is part of FDSTools, data analysis tools for Next
# Generation Sequencing of forensic DNA markers.
......@@ -57,7 +57,7 @@ from ..lib import split_quoted_string, DEF_TAG_EXPR, DEF_TAG_FORMAT, get_tag, \
from ConfigParser import RawConfigParser, NoSectionError, NoOptionError
__version__ = "1.0.3"
__version__ = "1.0.4"
# Pattern that matches a long argparse argument name.
......@@ -865,8 +865,7 @@ def add_arguments(parser):
help="library file containing marker definitions")
group.add_argument("-s", "--in-sample-raw", metavar="FASTA",
help="[ref-sample, case-sample] FastA or FastQ file containing raw "
"sequence data of the sample; if it is a FastQ file, be sure to "
"include 'is-fastq=yes' in the [tssv] section of your INI file")
"sequence data of the sample")
group.add_argument("-m", "--in-stuttermodel", metavar="STUT",
help="[case-sample] file containing a trained stutter model")
group.add_argument("-p", "--in-bgprofiles", metavar="PROFILES",
......
This diff is collapsed.
To-do:
* Remove duplicate reads before alignment in TSSV: HUGE potential speedup.
* Group tools by function in the command line help and put Pipeline on top.
* Samplevis:
* Detect whether correction was performed; hide related columns if not.
......
#!/usr/bin/env python
#
# Copyright (C) 2016 Jerry Hoogenboom
# Copyright (C) 2019 Jerry Hoogenboom
#
# This file is part of FDSTools, data analysis tools for Next
# Generation Sequencing of forensic DNA markers.
......@@ -21,6 +21,7 @@
#
from setuptools import setup, find_packages
from setuptools.extension import Extension
requires = ["numpy"]
......@@ -43,6 +44,10 @@ import fdstools as distmeta
x = setup(
name="fdstools",
packages=find_packages(),
ext_modules=[
Extension('fdstools.sg_align',
sources=['fdstools/sg_align.c'],
extra_compile_args=['-O3'])],
package_data={
"fdstools": ["vis/*.*", "vis/*/*"]
},
......
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