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Commit 5af85c81 authored by Workum, Dirk-Jan van's avatar Workum, Dirk-Jan van
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merge release_v4.0.0 into develop and solve merge conflicts

parents 5e6595f7 149a96db
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CHANGELOG.md
View file @ 5af85c81
......@@ -8,9 +8,11 @@ All notable changes to Pantools will be documented in this file.
### Changed
### Fixed
## [3.5] - TODO: add date for release
## [4.0.0] - TODO: add date for release
### Added
- CI/CD pipeline that for now only runs `mvn test` (merge request !41).
......@@ -62,8 +64,10 @@ All notable changes to Pantools will be documented in this file.
- Replaced method for Fisher exact test to correctly deal with larger values (merge request !66).
- `go_enrichment` no longer crashes when antiSMASH geneclusters were added to the pangenome (merge request !78).
- `add_annotations` now handles co-features correctly (merge request !79).
- Distinguish between homology groups as file or as list for `msa`, `core_snp_tree` and `consensus_tree` (merge request !86).
- `build_panproteome` no longer creates inconsistent 'header' and 'protein_ID' properties (merge request !89).
## [3.4] - 2021-05-04
## [3.4.0] - 2022-05-04
### Added
- Version and commit ID are reported when PanTools is initialized.
......
README.md
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......@@ -53,18 +53,18 @@ Note: tests are broken at the moment, which is why we're skipping the Maven test
-->
`mvn package` will generate two jar files in the `target/` directory.
The standalone jar file is named `pantools-<VERSION>.jar`, with `<VERSION>` being the PanTools version you have checked out.
To run it, use (we'll take version `3.4` as an example):
The standalone jar file is named `pantools-<version>.jar`, with `<version>` being the PanTools version you have checked out.
To run it, use:
```bash
java -jar target/pantools-3.4.jar -h
java -jar target/pantools-<version>.jar -h
```
Finally, we recommend making use of an alias to make running PanTools easier.
For example, add the following to your `~/.bashrc` file:
```bash
alias pantools="java -jar <PATH_TO_PANTOOLS>/target/pantools-3.4.jar"
alias pantools="java -jar <path/to/pantools>/target/pantools-<version>.jar"
```
where `<PATH_TO_PANTOOLS>` is the path to the directory where you checked out PanTools.
where `<path/to/pantools>` is the path to the directory where you checked out PanTools.
Then, you can run PanTools by simply typing `pantools` in your terminal.
## Contact
......
docs/source/conf.py
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......@@ -6,8 +6,8 @@ project = 'PanTools'
copyright = '2016, the PanTools team'
author = 'Sandra Smit'
release = '0.1'
version = '0.1.0'
release = '4,0.0'
version = '4,0.0'
# -- General configuration
......@@ -18,7 +18,8 @@ extensions = [
'sphinx.ext.autosummary',
'sphinx.ext.intersphinx',
'sphinx.ext.autosectionlabel',
'sphinx.ext.mathjax'
'sphinx.ext.mathjax',
'extensions.substitutioncodeblock'
]
intersphinx_mapping = {
......@@ -51,6 +52,9 @@ mathjax3_config = {'chtml': {'displayAlign': 'left',
# CSS files
html_css_files = ['css/custom.css', 'css/s5defs-roles.css']
# Code substitutions
substitutions = [('|ProjectVersion|', version)]
# Prolog
rst_prolog = """
.. include:: <s5defs.txt>
......@@ -60,4 +64,11 @@ rst_prolog = """
<br>
"""
\ No newline at end of file
"""
# Epilog
rst_epilog = """
.. |ProjectVersion| replace:: {versionnum}
""".format(
versionnum = version,
)
\ No newline at end of file
docs/source/construct.rst
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......@@ -784,7 +784,7 @@ database.
Functional databases
""""""""""""""""""""
Database versions in v3.4 repository
Database versions in v|ProjectVersion| repository
.. list-table::
:widths: 25 25 50
......@@ -1078,7 +1078,7 @@ Options
.. list-table::
:widths: 30 70
* - ```--annotations-file``/``-A``
* - ``--annotations-file``/``-A``
- A text file with the identifiers of annotations to be included,
each on a separate line. The most recent annotation is selected for
genomes without an identifier.
......
docs/source/extensions/substitutioncodeblock.py 0 → 100644
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"""
Custom Sphinx extension for code blocks allowing substitution.
"""
from typing import List
from sphinx.application import Sphinx
from sphinx.directives.code import CodeBlock
class SubstitutionCodeBlock(CodeBlock): # type: ignore
"""
Similar to CodeBlock but replaces placeholders with variables.
"""
def run(self) -> List:
"""
Replace placeholders with given variables.
"""
app = self.state.document.settings.env.app
new_content = []
self.content = self.content # type: List[str]
existing_content = self.content
for item in existing_content:
for pair in app.config.substitutions:
original, replacement = pair
item = item.replace(original, replacement)
new_content.append(item)
self.content = new_content
return list(CodeBlock.run(self))
def setup(app: Sphinx) -> None:
"""
Add the custom directives to Sphinx.
"""
app.add_config_value('substitutions', [], 'html')
app.add_directive('substitution-code-block', SubstitutionCodeBlock)
\ No newline at end of file
docs/source/index.rst
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PanTools version 3.5
PanTools version |ProjectVersion|
====================
PanTools is a toolkit for comparative analysis of large number of
......@@ -65,9 +65,9 @@ Add the path to the java archive of PanTools, located in the
*pantools/target* subdirectory, to the OS path environment variable.
Then run PanTools from the command line by:
.. code:: bash
.. substitution-code-block:: bash
$ java <JVM options> -jar pantools-3.4.jar <subcommand> <arguments>
$ java <JVM options> -jar pantools-|ProjectVersion|.jar <subcommand> <arguments>
| **Useful JVM options**
| - **-server** : To optimize JIT compilations for higher performance
......
docs/source/install.rst
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......@@ -12,19 +12,17 @@ For PanTools developers:
Download PanTools
-----------------
Clone PanTools from our repository and checkout to the 3.4 release branch.
Clone PanTools v|ProjectVersion| from our repository.
.. code:: bash
.. substitution-code-block:: bash
$ git clone https://git.wur.nl/bioinformatics/pantools
$ cd pantools
$ git checkout pantools_v3.4
$ git clone --branch v|ProjectVersion| https://git.wur.nl/bioinformatics/pantools
Test if PanTools is executable.
.. code:: bash
.. substitution-code-block:: bash
$ java -jar target/pantools-3.4.jar
$ java -jar target/pantools-|ProjectVersion|.jar
If the help page does not appear this (likely) means you don't have a
properly working Java version 8. Java is included in the PanTools conda
......@@ -41,16 +39,16 @@ command. Always include the **full** path to PanTools' .jar file.
If Java is set to your $PATH.
.. code:: bash
.. substitution-code-block:: bash
$ echo "alias pantools='java -Xms20g -Xmx50g -jar /YOUR_FULL_PATH/pantools/target/pantools-3.4.jar'" >> ~/.bashrc
$ echo "alias pantools='java -Xms20g -Xmx50g -jar /YOUR_FULL_PATH/pantools/target/pantools-|ProjectVersion|.jar'" >> ~/.bashrc
If Java is not set to your $PATH, include the **full** path in the
alias. Replace 'YOUR_PATH' 2x with the correct directory structure.
.. code:: bash
.. substitution-code-block:: bash
$ echo "alias pantools='/YOUR_PATH/jdk1.8.0_161/bin/java -Xms20g -Xmx50g -jar /YOUR_PATH/pantools/target/pantools-3.4.jar'" >> ~/.bashrc
$ echo "alias pantools='/YOUR_PATH/jdk1.8.0_161/bin/java -Xms20g -Xmx50g -jar /YOUR_PATH/pantools/target/pantools-|ProjectVersion|.jar'" >> ~/.bashrc
Source your ~/.bashrc and test if the alias works.
......
docs/source/msa.rst
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......@@ -30,7 +30,8 @@ created with **FastTree**.
from the list above requires use of the ``--method`` argument. For
aligning multiple homology groups, please use
``--method=multiple-groups`` with the homology groups specified in a
csv file on a single line (can be added with ``--homology-file=/path/to/hm.csv``.
csv file on a single line (can be added with
``--homology-file=/path/to/hm.csv`` or ``--homology-groups=2,3,4,4``).
For aligning regions, please use ``--method=regions`` with a regions
file that is added with ``--regions-file=/path/to/rf.txt``. For aligning
sequences based on a functional domain, please use
......@@ -99,7 +100,10 @@ Options
- Exclude a selection of genomes.
* - ``--homology-file``/``-H``
- A text file with homology group node identifiers, separated by a comma.
Default is all homology groups.
Default is all homology groups. (Mutually exclusive with ``--homology-groups``.)
* - ``--homology-groups``/``-G``
- A comma separated list of homology group node identifiers.
Default is all homology groups. (Mutually exclusive with ``--homology-file``.)
* - ``--regions-file``/``-R``
- A text file containing genome locations with on each line: a genome
number, sequence number, begin and end position, separated by a space.
......
docs/source/phylogeny.rst
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......@@ -18,7 +18,7 @@ All functions produce tree files in Newick format that can be visualized
with iTOL or any other phylogenetic tree visualization software.
- :ref:`phylogeny:rename phylogeny`
- :ref:`phylogeny:reroot phylogeny`
- :ref:`phylogeny:root phylogeny`
- :ref:`phylogeny:create tree template`
--------------
......@@ -79,6 +79,12 @@ Options
- A file with homology group node identifiers of single copy groups.
Default is single_copy_orthologs.csv, generated in the previous
:ref:`gene_classification <characterize:gene classification>` run.
(Mutually exclusive with ``--homology-groups``.)
* - ``--homology-groups``/``-G``
- A comma separated list of homology group node identifiers of single
copy groups. Default is single_copy_orthologs.csv, generated in
the previous :ref:`gene_classification <characterize:gene classification>` run.
(Mutually exclusive with ``--homology-file``.)
* - ``--protein``
- Use proteins instead of nucleotide sequences.
* - ``--phenotype``/``-p``
......@@ -210,9 +216,12 @@ Options
- Number of parallel working threads, default is the number of cores
or 8, whichever is lower.
* - ``--homology-file``/``-H``
- A file with homology group node identifiers. Default is
all_homology_groups.csv, generated in the previous
:ref:`gene_classification <characterize:gene classification>` run.
- A file with homology group node identifiers. Default is all
homology groups. (Mutually exclusive with ``--homology-groups``.)
* - ``--homology-groups``/``-G``
- A comma separated list of homology group node identifiers. Default
is all homology groups. (Mutually exclusive with
``--homology-file``.)
* - ``--polytomies``
- Allow polytomies for ASTRAL-PRO.
......
docs/source/tables/functional_databases.csv
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......@@ -2,7 +2,7 @@
go.basic.obo;GO;addons;http://purl.obolibrary.org/obo/go/go-basic.obo
gene_ontology.txt;Pfam;addons;ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases//Pfam35.0/database_files/gene_ontology.txt.gz
Pfam-A.clans.tsv;Pfam;addons;ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases//Pfam35.0/Pfam-A.clans.tsv.gz
interpro.xml;InterPro;addons;https://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz
interpro.xml;InterPro;addons;https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz
TIGRFAMS_GO_LINK;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMS_GO_LINK
TIGRFAMS_ROLE_LINK;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMS_ROLE_LINK
TIGR_ROLE_NAMES;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGR_ROLE_NAMES
......
docs/source/tutorial_part2.rst
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......@@ -21,7 +21,7 @@ or via wget.
We assume a PanTools alias was set during the
:ref:`installation <install:set pantools alias>`. This allows PanTools
to be executed with ``pantools`` rather than
``pantools/target/pantools-3.4.jar``. If you don’t have an alias, either
``pantools/target/pantools-|ProjectVersion|.jar``. If you don’t have an alias, either
set one or replace the pantools command with the full path to the .jar
file in the tutorials.
......
docs/source/tutorial_part4.rst
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......@@ -18,7 +18,7 @@ the following commands.
We assume a PanTools alias was set during the
:ref:`installation <install:set pantools alias>`. This allows PanTools
to be executed with ``pantools`` rather than
``pantools/target/pantools-3.4.jar``. If you don’t have an alias, either
``pantools/target/pantools-|ProjectVersion|.jar``. If you don’t have an alias, either
set one or replace the pantools command with the full path to the .jar
file in the tutorials.
......
pom.xml
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......@@ -6,7 +6,7 @@
<groupId>nl.wur.bif</groupId>
<artifactId>pantools</artifactId>
<version>3.4</version>
<version>4.0.0</version>
<properties>
<maven.compiler.source>8</maven.compiler.source>
......@@ -251,4 +251,4 @@
</plugin>
</plugins>
</build>
</project>
\ No newline at end of file
</project>
src/main/java/nl/wur/bif/pantools/cli/ConsensusTree.java
View file @ 5af85c81
package nl.wur.bif.pantools.cli;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.cli.mixins.ThreadNumber;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
import nl.wur.bif.pantools.pantools.Pantools;
import picocli.CommandLine.Model.CommandSpec;
import java.nio.file.Path;
import java.io.IOException;
import java.util.concurrent.Callable;
import static nl.wur.bif.pantools.cli.validation.Constraints.GraphDatabase;
import static nl.wur.bif.pantools.cli.validation.Constraints.InputFile;
import static nl.wur.bif.pantools.utils.Globals.*;
import static picocli.CommandLine.*;
......@@ -23,15 +23,12 @@ public class ConsensusTree implements Callable<Integer> {
@Spec CommandSpec spec;
@Mixin private ThreadNumber threadNumber;
@ArgGroup private SelectHmGroups selectHmGroups = new SelectHmGroups(); //needs to be initialized to prevent NullPointerException
@ParentCommand
@GraphDatabase
private Pantools pantools;
@Option(names = {"-H", "--homology-file"})
@InputFile(message = "{file.homology}")
Path homologyFile;
@Option(names = {"-l", "--log"}, hidden = true)
boolean log;
......@@ -39,22 +36,18 @@ public class ConsensusTree implements Callable<Integer> {
boolean polytomies;
@Override
public Integer call() {
public Integer call() throws IOException {
pantools.createLogger(spec);
new BeanValidation().argValidation(spec, this, threadNumber);
new BeanValidation().argValidation(spec, this, threadNumber, selectHmGroups);
pantools.setPangenomeGraph();
setGlobalParameters(); //TODO: use local parameters instead
phylogeny.consensus_tree();
phylogeny.consensus_tree(selectHmGroups.getHomologyGroups());
return 0;
}
private void setGlobalParameters() {
if (homologyFile != null) INPUT_FILE = homologyFile.toString();
THREADS = threadNumber.getnThreads();
LOG = log;
ALLOW_POLYTOMIES = polytomies;
}
}
src/main/java/nl/wur/bif/pantools/cli/CorePhylogeny.java
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......@@ -2,17 +2,17 @@ package nl.wur.bif.pantools.cli;
import jakarta.validation.constraints.Pattern;
import nl.wur.bif.pantools.cli.mixins.SelectGenomes;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.cli.mixins.ThreadNumber;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
import nl.wur.bif.pantools.pantools.Pantools;
import picocli.CommandLine.Model.CommandSpec;
import java.nio.file.Path;
import java.io.IOException;
import java.util.concurrent.Callable;
import static jakarta.validation.constraints.Pattern.Flag.CASE_INSENSITIVE;
import static nl.wur.bif.pantools.cli.validation.Constraints.GraphDatabase;
import static nl.wur.bif.pantools.cli.validation.Constraints.InputFile;
import static nl.wur.bif.pantools.utils.Globals.*;
import static picocli.CommandLine.*;
......@@ -27,15 +27,12 @@ public class CorePhylogeny implements Callable<Integer> {
@Spec CommandSpec spec;
@Mixin private ThreadNumber threadNumber;
@ArgGroup private SelectGenomes selectGenomes;
@ArgGroup private SelectHmGroups selectHmGroups = new SelectHmGroups(); //needs to be initialized to prevent NullPointerException
@ParentCommand
@GraphDatabase
private Pantools pantools;
@Option(names = {"-H", "--homology-file"})
@InputFile(message = "{file.homology}")
Path homologyFile;
@Option(names = "--protein")
boolean protein;
......@@ -47,24 +44,20 @@ public class CorePhylogeny implements Callable<Integer> {
String mode;
@Override
public Integer call() {
public Integer call() throws IOException {
pantools.createLogger(spec);
new BeanValidation().argValidation(spec, this, threadNumber, selectGenomes);
new BeanValidation().argValidation(spec, this, threadNumber, selectGenomes, selectHmGroups);
pantools.setPangenomeGraph();
setGlobalParameters(); //TODO: use local parameters instead
phylogeny.core_snp_tree();
phylogeny.core_snp_tree(selectHmGroups.getHomologyGroups());
return 0;
}
private void setGlobalParameters() {
setGenomeSelectionOptions(selectGenomes);
if (homologyFile != null) SELECTED_HMGROUPS = homologyFile.toString();
THREADS = threadNumber.getnThreads();
PHENOTYPE = phenotype;
CLUSTERING_METHOD = mode;
if (protein) Mode = "PROTEIN";
}
}
src/main/java/nl/wur/bif/pantools/cli/GroupInfo.java
View file @ 5af85c81
......@@ -2,12 +2,14 @@ package nl.wur.bif.pantools.cli;
import nl.wur.bif.pantools.cli.mixins.SelectGenomes;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.pantools.Pantools;
import java.nio.file.Path;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.stream.Collectors;
import static nl.wur.bif.pantools.cli.validation.Constraints.*;
import static nl.wur.bif.pantools.cli.validation.Constraints.Patterns.Flag.CASE_INSENSITIVE;
......@@ -24,15 +26,12 @@ public class GroupInfo implements Callable<Integer> {
@Spec Model.CommandSpec spec;
@ArgGroup private SelectGenomes selectGenomes;
@ArgGroup(multiplicity = "1") private SelectHmGroups selectHmGroups;
@ParentCommand
@GraphDatabase
private Pantools pantools;
@Parameters(descriptionKey = "homology-file", index = "0+")
@InputFile(message = "{file.homology}")
Path homologyFile;
@Option(names = "--functions")
void setFunctions(String value) {
functions = Arrays.asList(value.split(","));
......@@ -51,10 +50,9 @@ public class GroupInfo implements Callable<Integer> {
boolean obtainNodes;
@Override
public Integer call() {
public Integer call() throws IOException {
pantools.createLogger(spec);
new BeanValidation().argValidation(spec, this, selectGenomes);
new BeanValidation().argValidation(spec, this, selectGenomes, selectHmGroups);
pantools.setPangenomeGraph();
setGlobalParameters(); //TODO: use local parameters instead
......@@ -62,9 +60,10 @@ public class GroupInfo implements Callable<Integer> {
return 0;
}
private void setGlobalParameters() {
private void setGlobalParameters() throws IOException {
setGenomeSelectionOptions(selectGenomes);
SELECTED_HMGROUPS = homologyFile.toString();
SELECTED_HMGROUPS = selectHmGroups.getHomologyGroups().stream().map(String::valueOf).collect(Collectors.joining(","));
System.out.println("SELECTED_HMGROUPS = " + SELECTED_HMGROUPS);
if (genes != null) SELECTED_NAME = genes.toString().replaceAll("[\\[\\]]", "");
if (functions != null) SELECTED_LABEL = functions.toString().replaceAll("[\\[\\]]", "");
......
src/main/java/nl/wur/bif/pantools/cli/LocateGenes.java
View file @ 5af85c81
package nl.wur.bif.pantools.cli;
import jakarta.validation.constraints.Max;
import jakarta.validation.constraints.Min;
import nl.wur.bif.pantools.cli.mixins.SelectGenomes;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.pantools.Pantools;
import picocli.CommandLine.Command;
import picocli.CommandLine.Model.CommandSpec;
import java.nio.file.Path;
import jakarta.validation.constraints.Max;
import jakarta.validation.constraints.Min;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
import java.io.IOException;
import java.util.concurrent.Callable;
import java.util.stream.Collectors;
import static nl.wur.bif.pantools.cli.validation.Constraints.GraphDatabase;
import static nl.wur.bif.pantools.cli.validation.Constraints.InputFile;
import static nl.wur.bif.pantools.utils.Globals.*;
import static picocli.CommandLine.*;
......@@ -25,15 +28,12 @@ public class LocateGenes implements Callable<Integer> {
@Spec CommandSpec spec;
@ArgGroup private SelectGenomes selectGenomes;
@ArgGroup(multiplicity = "1") private SelectHmGroups selectHmGroups;
@ParentCommand
@GraphDatabase
private Pantools pantools;
@Parameters(descriptionKey = "homology-file", index = "0+")
@InputFile(message = "{file.homology}")
Path homologyFile;
@Option(names = {"-p", "--phenotype"})
String phenotype;
......@@ -54,10 +54,9 @@ public class LocateGenes implements Callable<Integer> {
boolean ignoreDuplications;
@Override
public Integer call() {
public Integer call() throws IOException {
pantools.createLogger(spec);
new BeanValidation().argValidation(spec, this, selectGenomes);
new BeanValidation().argValidation(spec, this, selectGenomes, selectHmGroups);
pantools.setPangenomeGraph("pangenome");
setGlobalParameters(); //TODO: use local parameters instead
......@@ -65,9 +64,10 @@ public class LocateGenes implements Callable<Integer> {
return 0;
}
private void setGlobalParameters() {
private void setGlobalParameters() throws IOException {
setGenomeSelectionOptions(selectGenomes);
SELECTED_HMGROUPS = homologyFile.toString();
SELECTED_HMGROUPS = selectHmGroups.getHomologyGroups().stream().map(String::valueOf).collect(Collectors.joining(","));
System.out.println("SELECTED_HMGROUPS = " + SELECTED_HMGROUPS);
core_threshold = coreThreshold;
PHENOTYPE = phenotype;
if (ignoreDuplications) Mode = "IGNORE-COPIES";
......
src/main/java/nl/wur/bif/pantools/cli/MSA.java
View file @ 5af85c81
......@@ -5,11 +5,13 @@ import jakarta.validation.constraints.Min;
import jakarta.validation.constraints.Pattern;
import nl.wur.bif.pantools.cli.mixins.SelectGenomes;
import nl.wur.bif.pantools.cli.mixins.ThreadNumber;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
import nl.wur.bif.pantools.pangenome.MultipleSequenceAlignment;
import nl.wur.bif.pantools.pantools.Pantools;
import picocli.CommandLine.Model.CommandSpec;
import java.io.IOException;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
......@@ -37,15 +39,12 @@ public class MSA implements Callable<Integer> {
@Spec CommandSpec spec;
@Mixin private ThreadNumber threadNumber;
@ArgGroup private SelectGenomes selectGenomes;
@ArgGroup private SelectHmGroups selectHmGroups = new SelectHmGroups(); //needs to be initialized to prevent NullPointerException
@ParentCommand
@GraphDatabase
private Pantools pantools;
@Option(names = {"-H", "--homology-file"})
@InputFile(message = "{file.homology}")
Path homologyFile;
@Option(names = {"-R", "--regions-file"})
@InputFile(message = "{file.regions}")
Path regionsFile;
......@@ -88,10 +87,9 @@ public class MSA implements Callable<Integer> {
boolean variants;
@Override
public Integer call() {
public Integer call() throws IOException {
pantools.createLogger(spec);
new BeanValidation().argValidation(spec, this, threadNumber, selectGenomes);
new BeanValidation().argValidation(spec, this, threadNumber, selectGenomes, selectHmGroups);
pantools.setPangenomeGraph();
method = method.replace("-", "_");