Merge pull request #238 from TheJacksonLaboratory/release-v1.0.4

Release v1.0.4

CHANGELOG.rst

@@ -2,6 +2,15 @@
 Changelog
 =========
 
+------
+v1.0.4
+------
+
+- ``SvAnna``
+  - update dependency versions.
+- ``svanna-io``
+  - Fix issue with VCF files compressed by newer compressor versions
+
 ------
 v1.0.3
 ------

README.md

@@ -9,7 +9,51 @@ Efficient and accurate pathogenicity prediction for coding and regulatory struct
 Most users should download the latest SvAnna distribution ZIP file from
 the [Releases page](https://github.com/TheJacksonLaboratory/SvAnna/releases).
 
-Please consult the Read the docs site for detailed documentation:
+## Example use
+
+SvAnna is a standalone command-line Java application and can be run as follows:
+
+```shell
+java -jar svanna-cli.jar -d path/to/svanna/data \
+  -t HP:0008330 \
+  --vcf example.vcf.gz \
+  --output-format html,csv,vcf
+```
+
+The analysis will filter out common SVs and perform phenotype-driven prioritization of the remaining SVs. 
+The SVs are assigned with *"Pathogenicity of Structural variation"* (PSV) score and written into 
+one of several output formats, such as CSV table, a VCF file, or a detailed HTML report.
+
+### HTML report
+
+The HTML report includes a header with the analysis summary and the SVs ordered by the PSV score 
+with the best scores on top.
+
+### Analysis summary
+
+The summary presents the clinical features encoded into terms of Human Phenotype Ontology (HPO) as well as 
+the other analysis parameters.
+
+![Analysis summary](img/analysis-summary.png)
+
+### Variant counts
+
+The report further breaks down SVs into several categories:
+
+![Variant counts](img/variant-counts.png)
+
+### Structural variants
+
+Last, each SV is presented in the context of the overlapping genes and transcripts:
+![Variant transcript summary](img/variant-tx-summary.png)
+
+We also show the variant in context of the neighboring repetitive regions and genes/transcripts:
+![Variant context](img/variant-tx-context.png)
+
+
+## Read more
+
+Please consult the Read the docs site for a detailed documentation:
 - [stable version](https://svanna.readthedocs.io/en/master) describing the latest release at the *Releases page*, or
 - [latest version](https://svanna.readthedocs.io/en/latest) summarizing the latest development on `development` branch.
 

docs/conf.py

@@ -56,7 +56,7 @@
 # The short X.Y version.
 version = u'1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'1.0.3'
+release = u'1.0.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pom.xml

@@ -16,7 +16,7 @@
         <module>svanna-benchmark</module>
     </modules>
     <groupId>org.monarchinitiative.svanna</groupId>
-    <version>1.0.3</version>
+    <version>1.0.4</version>
     <name>SvAnna</name>
 
     <parent>
@@ -34,7 +34,13 @@
 
         <phenol.version>2.0.0</phenol.version>
         <phenopacket-tools.version>1.0.0-RC2</phenopacket-tools.version>
+        <phenopacket-schema.version>2.0.2</phenopacket-schema.version>
         <silent.genes.version>0.2.5</silent.genes.version>
+        <htsjdk.version>3.0.5</htsjdk.version>
+        <commons-csv.version>1.7</commons-csv.version>
+        <commons-io.version>2.8.0</commons-io.version>
+        <commons-net.version>3.8.0</commons-net.version>
+        <commons-compress.version>1.24.0</commons-compress.version>
         <h2.version>1.4.200</h2.version>
     </properties>
 
@@ -111,7 +117,7 @@
             <dependency>
                 <groupId>org.phenopackets</groupId>
                 <artifactId>phenopacket-schema</artifactId>
-                <version>2.0.2</version>
+                <version>${phenopacket-schema.version}</version>
             </dependency>
             <dependency>
                 <groupId>com.google.protobuf</groupId>
@@ -131,7 +137,7 @@
             <dependency>
                 <groupId>com.github.samtools</groupId>
                 <artifactId>htsjdk</artifactId>
-                <version>3.0.5</version>
+                <version>${htsjdk.version}</version>
                 <exclusions>
                     <exclusion>
                         <groupId>org.tukaani</groupId>
@@ -143,22 +149,22 @@
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-csv</artifactId>
-                <version>1.7</version>
+                <version>${commons-csv.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-compress</artifactId>
-                <version>1.21</version>
+                <version>${commons-compress.version}</version>
             </dependency>
             <dependency>
                 <groupId>commons-io</groupId>
                 <artifactId>commons-io</artifactId>
-                <version>2.8.0</version>
+                <version>${commons-io.version}</version>
             </dependency>
             <dependency>
                 <groupId>commons-net</groupId>
                 <artifactId>commons-net</artifactId>
-                <version>3.8.0</version>
+                <version>${commons-net.version}</version>
             </dependency>
             <dependency>
                 <groupId>info.picocli</groupId>

svanna-benchmark/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

svanna-benchmark/src/main/java/org/monarchinitiative/svanna/benchmark/cmd/benchmark_case/BenchmarkCaseCommand.java

@@ -1,6 +1,5 @@
 package org.monarchinitiative.svanna.benchmark.cmd.benchmark_case;
 
-import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVPrinter;
 import org.monarchinitiative.svanna.benchmark.cmd.BaseBenchmarkCommand;
@@ -34,6 +33,7 @@
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
+import java.util.zip.GZIPOutputStream;
 
 @CommandLine.Command(name = "benchmark-case",
         aliases = {"BC"},
@@ -191,7 +191,7 @@ private void writeOutResults(File output, BenchmarkResults results, Set<String>
 
         // "case_name", "background_vcf", "variant_id", "rank", "vtype", "is_causal", "priority"
         LOGGER.info("Writing the results for `{}`", results.caseName());
-        try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new GzipCompressorOutputStream(new FileOutputStream(output))))) {
+        try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(output))))) {
             CSVPrinter printer = CSVFormat.DEFAULT
                     .withHeader("case_name", "background_vcf", "variant_id", "rank", "vtype", "is_causal", "priority")
                     .print(writer);

svanna-cli/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>svanna-cli</artifactId>

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

@@ -17,7 +17,7 @@
         footer = Main.FOOTER)
 public class Main implements Callable<Integer>  {
 
-    public static final String VERSION = "svanna-cli v1.0.3";
+    public static final String VERSION = "svanna-cli v1.0.4";
 
     public static final int WIDTH = 120;
 

svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/tabular/TabularResultWriter.java

@@ -1,6 +1,5 @@
 package org.monarchinitiative.svanna.cli.writer.tabular;
 
-import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVPrinter;
 import org.monarchinitiative.svanna.cli.writer.AnalysisResults;
@@ -27,6 +26,7 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.function.Consumer;
+import java.util.zip.GZIPOutputStream;
 
 public class TabularResultWriter implements ResultWriter {
 
@@ -63,7 +63,7 @@ private BufferedWriter openWriter(Path output, String prefix) throws IOException
         Path outPath = output.resolve(prefix + suffix + (compress ? ".gz" : ""));
         LogUtils.logInfo(LOGGER, "Writing tabular results into {}", outPath.toAbsolutePath());
         return compress
-                ? new BufferedWriter(new OutputStreamWriter(new GzipCompressorOutputStream(new FileOutputStream(outPath.toFile()))))
+                ? new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(outPath.toFile()))))
                 : Files.newBufferedWriter(outPath);
     }
 

svanna-configuration/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

svanna-core/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

svanna-db/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

svanna-ingest/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>svanna-ingest</artifactId>

svanna-ingest/src/main/java/org/monarchinitiative/svanna/ingest/cmd/BuildDb.java

@@ -7,8 +7,6 @@
 import org.apache.commons.codec.digest.MessageDigestAlgorithms;
 import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
 import org.apache.commons.compress.archivers.zip.ZipFile;
-import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
-import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
@@ -87,6 +85,8 @@
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
 
 @CommandLine.Command(name = "build-db",
         aliases = "B",
@@ -369,7 +369,7 @@ private static List<? extends GencodeGene> downloadAndPreprocessGenes(GeneProper
         GeneParser jsonParser = parserFactory.forFormat(SerializationFormat.JSON);
         Path destination = buildDir.resolve("gencode.v38.genes.json.gz");
         LOGGER.info("Serializing the genes to {}", destination.toAbsolutePath());
-        try (OutputStream os = new BufferedOutputStream(new GzipCompressorOutputStream(Files.newOutputStream(destination)))) {
+        try (OutputStream os = new BufferedOutputStream(new GZIPOutputStream(Files.newOutputStream(destination)))) {
             jsonParser.write(genes, os);
         }
 
@@ -563,7 +563,7 @@ private static Map<Integer, Integer> parseNcbiToHgncTable(String ncbiGeneToHgnc)
 
     private static BufferedReader openForReading(Path tablePath) throws IOException {
         return (tablePath.toFile().getName().endsWith(".gz"))
-                ? new BufferedReader(new InputStreamReader(new GzipCompressorInputStream(Files.newInputStream(tablePath))))
+                ? new BufferedReader(new InputStreamReader(new GZIPInputStream(Files.newInputStream(tablePath))))
                 : Files.newBufferedReader(tablePath);
 
     }

svanna-io/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.monarchinitiative.svanna</groupId>
-        <version>1.0.3</version>
+        <version>1.0.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

svanna-io/src/main/java/org/monarchinitiative/svanna/io/parse/VcfVariantParser.java

@@ -7,7 +7,6 @@
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderVersion;
-import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.monarchinitiative.svanna.core.LogUtils;
 import org.monarchinitiative.svanna.core.filter.FilterResult;
 import org.monarchinitiative.svanna.core.filter.FilterType;
@@ -23,15 +22,16 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.BufferedReader;
-import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Function;
 import java.util.stream.Stream;
+import java.util.zip.GZIPInputStream;
 
 /**
  * Parse variants stored in a VCF file. The parser is <em>NOT</em> thread safe!
@@ -97,20 +97,39 @@ public Stream<FullSvannaVariant> createVariantAlleles(Path filePath) throws IOEx
         VCFCodec codec = new VCFCodec();
         codec.setVCFHeader(header, header.getVCFHeaderVersion() == null ? VCFHeaderVersion.VCF4_1 : header.getVCFHeaderVersion());
 
-        BufferedReader reader;
-        if (filePath.toFile().getName().endsWith(".gz"))
-            reader = new BufferedReader(new InputStreamReader(new GzipCompressorInputStream(new FileInputStream(filePath.toFile()))));
-        else
-            reader = Files.newBufferedReader(filePath);
+        BufferedReader reader = openFileForReading(filePath);
 
         return reader.lines()
-                .onClose(() -> {try {reader.close();} catch (IOException ignored) {}})
+                .onClose(closeReader(reader))
                 .map(toVariantContext(codec))
                 .flatMap(Optional::stream)
                 .map(toVariants())
                 .flatMap(Optional::stream);
     }
 
+    private static BufferedReader openFileForReading(Path filePath) throws IOException {
+        BufferedReader reader;
+        if (filePath.toFile().getName().endsWith(".gz"))
+            reader = new BufferedReader(
+                    new InputStreamReader(
+                            new GZIPInputStream(Files.newInputStream(filePath)),
+                            StandardCharsets.UTF_8));
+        else
+            reader = Files.newBufferedReader(filePath, StandardCharsets.UTF_8);
+        return reader;
+    }
+
+    private static Runnable closeReader(BufferedReader reader) {
+        return () -> {
+            try {
+                LOGGER.trace("Closing VCF file");
+                reader.close();
+            } catch (IOException e) {
+                LOGGER.warn("Error while closing the VCF file", e);
+            }
+        };
+    }
+
     /**
      * One variant context might represent multiple sequence variants or a single symbolic variant/breakend.
      * This function melts the variant context to a collection of variants.

svanna-io/src/main/java/org/monarchinitiative/svanna/io/service/SilentGenesGeneService.java

@@ -1,6 +1,5 @@
 package org.monarchinitiative.svanna.io.service;
 
-import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.monarchinitiative.svanna.core.service.GeneService;
 import org.monarchinitiative.svanna.core.service.QueryResult;
 import org.monarchinitiative.svanna.io.service.jannovar.IntervalArray;
@@ -23,6 +22,7 @@
 import java.nio.file.Path;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.zip.GZIPInputStream;
 
 public class SilentGenesGeneService implements GeneService {
 
@@ -64,7 +64,7 @@ public static SilentGenesGeneService of(GenomicAssembly assembly, Path silentGen
     private static InputStream openForReading(Path silentGenesJsonPath) throws IOException {
         if (silentGenesJsonPath.toFile().getName().endsWith(".gz")) {
             LOGGER.debug("Assuming the file is gzipped");
-            return new BufferedInputStream(new GzipCompressorInputStream(Files.newInputStream(silentGenesJsonPath)));
+            return new BufferedInputStream(new GZIPInputStream(Files.newInputStream(silentGenesJsonPath)));
         } else {
             return new BufferedInputStream(Files.newInputStream(silentGenesJsonPath));
         }