Merge pull request #53 from TheJacksonLaboratory/release_v2.0.1

Release v2.0.1

.github/workflows/maven.yml

@@ -31,4 +31,4 @@ jobs:
           distribution: 'adopt'
 
       - name: Build with Maven
-        run: ./mvnw --batch-mode --update-snapshots verify
+        run: ./mvnw --quiet --batch-mode test

CHANGELOG.md

@@ -1,6 +1,12 @@
 # Changelog
 
-## ✈ latest
+## ✈ v2.0.1
+
+- `squirls-core`
+  - fix bug in allele generator leading to generation of bad splice site snippets for transcripts on negative strand 
+    in sequence trekker  
+
+## ✈ v2.0.0
 
 - `Squirls`
   - add `squirls-bootstrap` to quickly bootstrap Squirls even without Spring

Dockerfile

@@ -0,0 +1,10 @@
+FROM ubuntu:bionic
+
+RUN apt-get update && apt-get upgrade && apt-get -y install openjdk-11-jre \
+    procps
+
+COPY squirls-cli/target/squirls-cli-2.0.1.jar /opt/squirls/squirls-cli-2.0.1.jar
+COPY docker/squirls /opt/bin/squirls
+RUN chmod +x /opt/bin/squirls
+
+ENV PATH="/opt/bin:${PATH}"

HOW_TO_RELEASE.md

@@ -2,9 +2,10 @@
 
 Release checklist items:
 
-- update `CHANGELOG.md`, sync the content of `CHANGELOG.md` and `squirls-cli/CHANGELOG.md`
+- update `CHANGELOG.md`
 - update version in:
   - `pom.xml`
   - documentation
   - `org.monarchinitiative.squirls.cli.Main`
   - `org.monarchinitiative.squirls.ingest.Main`
+  - Dockerfile

README.md

@@ -1,5 +1,6 @@
 # SQUIRLS
 
+[![GitHub release](https://img.shields.io/github/release/TheJacksonLaboratory/Squirls.svg)](https://github.com/TheJacksonLaboratory/Squirls/releases)
 ![Java CI with Maven](https://github.com/TheJacksonLaboratory/Squirls/workflows/Java%20CI%20with%20Maven/badge.svg)
 [![Documentation Status](https://readthedocs.org/projects/squirls/badge/?version=latest)](https://squirls.readthedocs.io/en/master/?badge=master)
 

docker/squirls

@@ -0,0 +1,3 @@
+#!/bin/sh
+SQUIRLS_JAR=/opt/squirls/squirls-cli-2.0.0.jar
+java -jar ${SQUIRLS_JAR} ${@}

docs/conf.py

@@ -20,13 +20,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'Squirls'
-copyright = '2022, Daniel Danis, Peter N Robinson'
+copyright = '2023, Daniel Danis, Peter N Robinson'
 author = 'Daniel Danis, Peter N Robinson'
 
 # The short X.Y version
 version = '2.0'
 # The full version, including alpha/beta/rc tags
-release = 'v2.0.0'
+release = 'v2.0.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/running.rst

@@ -65,6 +65,8 @@ Squirls reports scores in four columns:
 - maximum Squirls pathogenicity prediction rounded up to 3 significant digits
 - Squirls pathogenicity predictions calculated for each transcript the variant overlaps with
 
+.. note::
+  The options ``--output-format``, ``--n-variants-to-report``, ``--out-dir``, ``--report-features`` are ignored.
 
 ``annotate-csv`` - Annotate variant positions stored in a CSV file
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -74,9 +76,9 @@ To annotate more than just a few variant positions, it may be more convenient to
 Let's run the ``annotate-csv`` command to annotate four variants stored in the `example.csv`_ file
 (an example CSV file with 4 variants stored in Squirls repository)::
 
-  java -jar squirls-cli.jar annotate-csv -d $SQUIRLS_DATA example.csv path/to/output/file
+  java -jar squirls-cli.jar annotate-csv -d $SQUIRLS_DATA example.csv output
 
-Squirls reads the variants and stores the scores into ``path/to/output/file.html`` file. The *HTML* is the default output format,
+Squirls reads the variants and stores the scores into ``output.html`` file. The *HTML* is the default output format,
 see :ref:`rstoutputformats` section for more details.
 
 Mandatory arguments
@@ -100,6 +102,7 @@ In addition to the mandatory arguments, Squirls allows to fine tune the annotati
   in all output formats. Default: ``html``
 * ``-n, --n-variants-to-report`` - number of most pathogenic variants to include in *HTML* report. The option has
   no effect on *VCF* output format. Default: ``100``
+* ``--out-dir`` - path to folder where to write the output files. Default: current working directory
 * ``--report-features`` - include Squirls features into the output. Default: ``false``
 * ``-t | --transcript-source`` - transcript source to use. Choose one of ``{REFSEQ, ENSEMBL, UCSC}``. Default: ``REFSEQ``
 * ``--threads`` - process variants on *n* threads. Default: ``2``
@@ -137,6 +140,7 @@ In addition to the mandatory arguments, Squirls allows to fine tune the annotati
   in all output formats. Default: ``html``
 * ``-n, --n-variants-to-report`` - number of most pathogenic variants to include in *HTML* report. The option has
   no effect on *VCF* output format. Default: ``100``
+* ``--out-dir`` - path to folder where to write the output files. Default: current working directory
 * ``--report-features`` - include Squirls features into the output. Default: ``false``
 * ``-t | --transcript-source`` - transcript source to use. Choose one of ``{REFSEQ, ENSEMBL, UCSC}``. Default: ``REFSEQ``
 * ``--threads`` - process variants on *n* threads. Default: ``2``

pom.xml

@@ -5,7 +5,7 @@
     <groupId>org.monarchinitiative.squirls</groupId>
     <artifactId>Squirls</artifactId>
     <packaging>pom</packaging>
-    <version>2.0.1-SNAPSHOT</version>
+    <version>2.0.1</version>
     <modules>
         <module>squirls-core</module>
         <module>squirls-io</module>
@@ -218,6 +218,14 @@
                     <artifactId>maven-wrapper-plugin</artifactId>
                     <version>3.0.1</version>
                 </plugin>
+                <plugin>
+                    <groupId>org.codehaus.mojo</groupId>
+                    <artifactId>versions-maven-plugin</artifactId>
+                    <version>2.8.1</version>
+                    <configuration>
+                        <generateBackupPoms>false</generateBackupPoms>
+                    </configuration>
+                </plugin>
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-source-plugin</artifactId>
@@ -270,6 +278,10 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
             </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>versions-maven-plugin</artifactId>
+            </plugin>
         </plugins>
     </build>
 

squirls-bootstrap/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <artifactId>Squirls</artifactId>
         <groupId>org.monarchinitiative.squirls</groupId>
-        <version>2.0.1-SNAPSHOT</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

squirls-cli/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>Squirls</artifactId>
         <groupId>org.monarchinitiative.squirls</groupId>
-        <version>2.0.1-SNAPSHOT</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/Main.java

@@ -100,7 +100,7 @@
         footer = Main.FOOTER)
 public class Main implements Callable<Integer> {
 
-    public static final String VERSION = "squirls v1.0.1-SNAPSHOT";
+    public static final String VERSION = "squirls v2.0.1";
 
     public static final int WIDTH = 120;
 

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/cmd/AnnotatingSquirlsCommand.java

@@ -79,6 +79,7 @@
 import org.monarchinitiative.squirls.cli.writers.*;
 import picocli.CommandLine;
 
+import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -97,6 +98,10 @@ public abstract class AnnotatingSquirlsCommand extends SquirlsCommand {
             description = "Compress the output (default: ${DEFAULT-VALUE})")
     public boolean compress = false;
 
+    @CommandLine.Option(names = {"--out-dir"},
+            description = "Path to folder where to write the output files (default: current working directory).")
+    public Path outDir = Path.of("");
+
     @CommandLine.Option(names = {"-f", "--output-format"},
             paramLabel = "html",
             description = "Comma separated list of output formats to use for writing the results (default: ${DEFAULT-VALUE})")
@@ -133,18 +138,22 @@ protected static Collection<OutputFormat> parseOutputFormats(String outputFormat
         return formats;
     }
 
-    protected OutputOptions prepareOutputOptions(Path outputPrefix) throws IOException {
+    protected OutputOptions prepareOutputOptions(String prefix) throws IOException {
+        if (prefix.contains(File.separator)) {
+            // +1 to exclude the separator
+            prefix = prefix.substring(prefix.lastIndexOf(File.separator)+1);
+            LOGGER.warn("The prefix '{}' contains the file separator character '{}'. The CLI has changed, please provide the path to the output directory using the `--out-dir` option. Using the last part of the string as the prefix '{}'.", prefix, File.separator, prefix);
+        }
+
         // Ensure the parent folders exist or explode.
-        if (Files.isDirectory(outputPrefix)) {
-            LOGGER.warn("Provided output prefix points to an existing directory. Results will be stored at {}/squirls*", outputPrefix.toAbsolutePath());
-            outputPrefix = outputPrefix.resolve("squirls");
+        if (!Files.isDirectory(outDir)) {
+            LOGGER.info("The output directory {} does not exist. Creating the missing directories.", outDir.toAbsolutePath());
+            Files.createDirectories(outDir);
         }
-        Path parent = outputPrefix.getParent();
-        if (!Files.isDirectory(parent))
-            Files.createDirectories(parent);
 
         return OutputOptions.builder()
-                .setOutputPrefix(outputPrefix)
+                .setOutputDirectory(outDir)
+                .setPrefix(prefix)
                 .addOutputFormats(parseOutputFormats(outputFormats))
                 .setCompress(compress)
                 .setReportFeatures(reportFeatures)

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/cmd/annotate_csv/AnnotateCsvCommand.java

@@ -135,9 +135,8 @@ public class AnnotateCsvCommand extends AnnotatingSquirlsCommand {
     public Path inputPath;
 
     @CommandLine.Parameters(index = "1",
-            paramLabel = "output",
             description = "Prefix for the output files")
-    public Path outputPrefix = Path.of("output");
+    public String outputPrefix;
 
     private static GenomicVariant parseCsvRecord(GenomicAssembly assembly, CSVRecord record) throws SquirlsException {
         // parse contig

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/cmd/annotate_vcf/AnnotateVcfCommand.java

@@ -97,7 +97,6 @@
 import org.monarchinitiative.squirls.core.SquirlsResult;
 import org.monarchinitiative.squirls.core.VariantSplicingEvaluator;
 import org.monarchinitiative.squirls.core.reference.SplicingPwmData;
-import org.monarchinitiative.squirls.io.SquirlsResourceException;
 import org.monarchinitiative.svart.*;
 import org.monarchinitiative.svart.assembly.GenomicAssembly;
 import org.monarchinitiative.vmvt.core.VmvtGenerator;
@@ -134,9 +133,8 @@ public class AnnotateVcfCommand extends AnnotatingSquirlsCommand {
     public Path inputPath;
 
     @CommandLine.Parameters(index = "1",
-            paramLabel = "output",
             description = "Prefix for the output files.")
-    public Path outputPrefix = Path.of("output");
+    public String prefix;
 
     private static Function<VariantContext, Collection<VariantContext>> meltToSingleAltVariants() {
         return vc -> {
@@ -318,7 +316,7 @@ public Integer call() {
                     .addAllVariants(annotated)
                     .build();
 
-            analysisResultsWriter.writeResults(results, prepareOutputOptions(outputPrefix));
+            analysisResultsWriter.writeResults(results, prepareOutputOptions(prefix));
         } catch (Exception e) {
             LOGGER.error("Error: ", e);
             return 1;

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/writers/AnalysisResultsWriterDefault.java

@@ -104,7 +104,7 @@ public void writeResults(AnalysisResults results, OutputOptions options) {
         for (OutputFormat format : options.outputFormats()) {
             ResultWriter writer = resultWriterForFormat(format, options.compress(), options.reportFeatures(), options.reportAllTranscripts());
             try {
-                writer.write(results, options.outputPrefix());
+                writer.write(results, options);
             } catch (IOException e) {
                 LOGGER.error("Error writing {} results: {}", format, e.getMessage());
             }

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/writers/OutputOptions.java

@@ -88,14 +88,16 @@ public class OutputOptions {
     private final boolean reportFeatures;
     private final boolean reportAllTranscripts;
     private final Set<OutputFormat> outputFormats;
-    private final Path outputPrefix;
+    private final Path outputDirectory;
+    private final String prefix;
 
     private OutputOptions(Builder builder) {
         this.compress = builder.compress;
         this.reportFeatures = builder.reportFeatures;
         this.reportAllTranscripts = builder.reportAllTranscripts;
         this.outputFormats = Set.copyOf(builder.outputFormats);
-        this.outputPrefix = Objects.requireNonNull(builder.outputPrefix);
+        this.outputDirectory = Objects.requireNonNull(builder.outputDirectory);
+        this.prefix = Objects.requireNonNull(builder.prefix);
     }
 
     public static Builder builder() {
@@ -118,21 +120,12 @@ public Set<OutputFormat> outputFormats() {
         return outputFormats;
     }
 
-    public Path outputPrefix() {
-        return outputPrefix;
+    public Path outputDirectory() {
+        return outputDirectory;
     }
 
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
-        OutputOptions that = (OutputOptions) o;
-        return compress == that.compress && reportFeatures == that.reportFeatures && reportAllTranscripts == that.reportAllTranscripts && Objects.equals(outputFormats, that.outputFormats) && Objects.equals(outputPrefix, that.outputPrefix);
-    }
-
-    @Override
-    public int hashCode() {
-        return Objects.hash(compress, reportFeatures, reportAllTranscripts, outputFormats, outputPrefix);
+    public String prefix() {
+        return prefix;
     }
 
     @Override
@@ -142,7 +135,8 @@ public String toString() {
                 ", reportFeatures=" + reportFeatures +
                 ", reportAllTranscripts=" + reportAllTranscripts +
                 ", outputFormats=" + outputFormats +
-                ", outputPrefix='" + outputPrefix + '\'' +
+                ", outputDirectory=" + outputDirectory +
+                ", prefix='" + prefix + '\'' +
                 '}';
     }
 
@@ -152,7 +146,8 @@ public static class Builder {
         private boolean compress = false;
         private boolean reportFeatures = false;
         private boolean reportAllTranscripts = false;
-        private Path outputPrefix = Path.of("output");
+        private Path outputDirectory;
+        private String prefix;
 
         private Builder() {
         }
@@ -172,8 +167,13 @@ public Builder setReportAllTranscripts(boolean reportAllTranscripts) {
             return this;
         }
 
-        public Builder setOutputPrefix(Path outputPrefix) {
-            this.outputPrefix = outputPrefix;
+        public Builder setOutputDirectory(Path outputDirectory) {
+            this.outputDirectory = outputDirectory;
+            return this;
+        }
+
+        public Builder setPrefix(String prefix) {
+            this.prefix = prefix;
             return this;
         }
 

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/writers/ResultWriter.java

@@ -80,7 +80,6 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
-import java.nio.file.Path;
 
 /**
  * Implementors write {@link AnalysisResults} in different formats.
@@ -90,5 +89,5 @@ public interface ResultWriter {
 
     Logger LOGGER = LoggerFactory.getLogger(ResultWriter.class);
 
-    void write(AnalysisResults results, Path prefix) throws IOException;
+    void write(AnalysisResults results, OutputOptions outputOptions) throws IOException;
 }

squirls-cli/src/main/java/org/monarchinitiative/squirls/cli/writers/html/HtmlResultWriter.java

@@ -79,10 +79,7 @@
 import de.charite.compbio.jannovar.annotation.VariantAnnotations;
 import org.monarchinitiative.squirls.cli.visualization.SplicingVariantGraphicsGenerator;
 import org.monarchinitiative.squirls.cli.visualization.VisualizableVariantAllele;
-import org.monarchinitiative.squirls.cli.writers.AnalysisResults;
-import org.monarchinitiative.squirls.cli.writers.OutputFormat;
-import org.monarchinitiative.squirls.cli.writers.ResultWriter;
-import org.monarchinitiative.squirls.cli.writers.WritableSplicingAllele;
+import org.monarchinitiative.squirls.cli.writers.*;
 import org.monarchinitiative.squirls.core.SquirlsResult;
 import org.monarchinitiative.svart.CoordinateSystem;
 import org.monarchinitiative.svart.GenomicVariant;
@@ -95,7 +92,6 @@
 import java.io.Writer;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.text.NumberFormat;
 import java.util.ArrayList;
 import java.util.Comparator;
@@ -141,8 +137,8 @@ private static String getRepresentation(WritableSplicingAllele writableSplicingA
     }
 
     @Override
-    public void write(AnalysisResults results, Path prefix) throws IOException {
-        Path outputPath = Paths.get(prefix.toAbsolutePath().toString() + '.' + OutputFormat.HTML.getFileExtension());
+    public void write(AnalysisResults results, OutputOptions outputOptions) throws IOException {
+        Path outputPath = outputOptions.outputDirectory().resolve(outputOptions.prefix() + '.' + OutputFormat.HTML.getFileExtension());
         LOGGER.info("Writing HTML output to `{}`", outputPath);
 
         // sort results by max squirls pathogenicity and select at most n variants