org.opencb.opencga.client.rest.clients.AlignmentClient Maven / Gradle / Ivy
/*
* Copyright 2015-2024 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.opencga.client.rest.clients;
import org.ga4gh.models.ReadAlignment;
import org.opencb.biodata.models.alignment.GeneCoverageStats;
import org.opencb.biodata.models.alignment.RegionCoverage;
import org.opencb.commons.datastore.core.ObjectMap;
import org.opencb.opencga.client.config.ClientConfiguration;
import org.opencb.opencga.client.exceptions.ClientException;
import org.opencb.opencga.client.rest.*;
import org.opencb.opencga.core.models.alignment.AlignmentGeneCoverageStatsParams;
import org.opencb.opencga.core.models.alignment.AlignmentIndexParams;
import org.opencb.opencga.core.models.alignment.AlignmentQcParams;
import org.opencb.opencga.core.models.alignment.BwaWrapperParams;
import org.opencb.opencga.core.models.alignment.CoverageIndexParams;
import org.opencb.opencga.core.models.alignment.DeeptoolsWrapperParams;
import org.opencb.opencga.core.models.alignment.FastqcWrapperParams;
import org.opencb.opencga.core.models.alignment.PicardWrapperParams;
import org.opencb.opencga.core.models.alignment.SamtoolsWrapperParams;
import org.opencb.opencga.core.models.job.Job;
import org.opencb.opencga.core.response.RestResponse;
/*
* WARNING: AUTOGENERATED CODE
*
* This code was generated by a tool.
*
* Manual changes to this file may cause unexpected behavior in your application.
* Manual changes to this file will be overwritten if the code is regenerated.
*/
/**
* This class contains methods for the Alignment webservices.
* PATH: analysis/alignment
*/
public class AlignmentClient extends AbstractParentClient {
public AlignmentClient(String token, ClientConfiguration configuration) {
super(token, configuration);
}
/**
* BWA is a software package for mapping low-divergent sequences against a large reference genome.
* @param data BWA parameters.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runBwa(BwaWrapperParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/bwa", null, "run", params, POST, Job.class);
}
/**
* Compute coverage for a list of alignment files.
* @param data Coverage computation parameters.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runCoverageIndex(CoverageIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/coverage/index", null, "run", params, POST, Job.class);
}
/**
* Compute gene coverage stats for a given alignment file and a list of genes.
* @param data Gene coverage stats parameters for a given BAM file and a list of genes.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse coverageQcGeneCoverageStatsRun(AlignmentGeneCoverageStatsParams data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/coverage/qc/geneCoverageStats", null, "run", params, POST, Job.class);
}
/**
* Query the coverage of an alignment file for regions or genes.
* @param file File ID.
* @param params Map containing any of the following optional parameters.
* study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
* region: Comma separated list of regions 'chr:start-end, e.g.: 2,3:63500-65000.
* gene: Comma separated list of genes, e.g.: BCRA2,TP53.
* offset: Offset to extend the region, gene or exon at up and downstream.
* onlyExons: Only exons are taking into account when genes are specified.
* range: Range of coverage values to be reported. Minimum and maximum values are separated by '-', e.g.: 20-40 (for coverage
* values greater or equal to 20 and less or equal to 40). A single value means to report coverage values less or equal to
* that value.
* windowSize: Window size for the region coverage (if a coverage range is provided, window size must be 1).
* splitResults: Split results into regions (or gene/exon regions).
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse queryCoverage(String file, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.putIfNotNull("file", file);
return execute("analysis", null, "alignment/coverage", null, "query", params, GET, RegionCoverage.class);
}
/**
* Compute coverage ratio from file #1 vs file #2, (e.g. somatic vs germline).
* @param file1 Input file #1 (e.g. somatic file).
* @param file2 Input file #2 (e.g. germline file).
* @param params Map containing any of the following optional parameters.
* study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
* skipLog2: Do not apply Log2 to normalise the coverage ratio.
* region: Comma separated list of regions 'chr:start-end, e.g.: 2,3:63500-65000.
* gene: Comma separated list of genes, e.g.: BCRA2,TP53.
* offset: Offset to extend the region, gene or exon at up and downstream.
* onlyExons: Only exons are taking into account when genes are specified.
* windowSize: Window size for the region coverage (if a coverage range is provided, window size must be 1).
* splitResults: Split results into regions (or gene/exon regions).
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse ratioCoverage(String file1, String file2, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.putIfNotNull("file1", file1);
params.putIfNotNull("file2", file2);
return execute("analysis", null, "alignment/coverage", null, "ratio", params, GET, RegionCoverage.class);
}
/**
* Compute coverage stats per transcript for a list of genes.
* @param file File ID.
* @param gene Comma separated list of genes, e.g.: BCRA2,TP53.
* @param params Map containing any of the following optional parameters.
* study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
* threshold: Only regions whose coverage depth is under this threshold will be reported.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse statsCoverage(String file, String gene, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.putIfNotNull("file", file);
params.putIfNotNull("gene", gene);
return execute("analysis", null, "alignment/coverage", null, "stats", params, GET, GeneCoverageStats.class);
}
/**
* Deeptools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as
* ChIP-seq, RNA-seq or MNase-seq.
* @param data Deeptools parameters. Supported Deeptools commands: bamCoverage, bamCompare.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runDeeptools(DeeptoolsWrapperParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/deeptools", null, "run", params, POST, Job.class);
}
/**
* A high throughput sequence QC analysis tool.
* @param data FastQC parameters.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runFastqc(FastqcWrapperParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/fastqc", null, "run", params, POST, Job.class);
}
/**
* Index alignment file.
* @param data Alignment index params.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runIndex(AlignmentIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/index", null, "run", params, POST, Job.class);
}
/**
* Picard is a set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as
* SAM/BAM/CRAM and VCF. Supported Picard commands: CollectHsMetrics, CollectWgsMetrics, BedToIntervalList.
* @param data Picard parameters. Supported Picard commands: CollectHsMetrics, CollectWgsMetrics, BedToIntervalList.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runPicard(PicardWrapperParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/picard", null, "run", params, POST, Job.class);
}
/**
* Compute quality control (QC) metrics for a given alignment file: samtools stats, samtools flag stats and FastQC metrics.
* @param data Alignment quality control (QC) parameters. It computes: stats, flag stats and fastqc metrics. The BAM file ID is
* mandatory and in order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runQc(AlignmentQcParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/qc", null, "run", params, POST, Job.class);
}
/**
* Search over indexed alignments.
* @param file File ID.
* @param params Map containing any of the following optional parameters.
* limit: Number of results to be returned.
* skip: Number of results to skip.
* count: Get the total number of results matching the query. Deactivated by default.
* study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
* region: Comma separated list of regions 'chr:start-end, e.g.: 2,3:63500-65000.
* gene: Comma separated list of genes, e.g.: BCRA2,TP53.
* offset: Offset to extend the region, gene or exon at up and downstream.
* onlyExons: Only exons are taking into account when genes are specified.
* minMappingQuality: Minimum mapping quality.
* maxNumMismatches: Maximum number of mismatches.
* maxNumHits: Maximum number of hits.
* properlyPaired: Return only properly paired alignments.
* maxInsertSize: Maximum insert size.
* skipUnmapped: Skip unmapped alignments.
* skipDuplicated: Skip duplicated alignments.
* regionContained: Return alignments contained within boundaries of region.
* forceMDField: Force SAM MD optional field to be set with the alignments.
* binQualities: Compress the nucleotide qualities by using 8 quality levels.
* splitResults: Split results into regions (or gene/exon regions).
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse query(String file, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.putIfNotNull("file", file);
return execute("analysis", null, "alignment", null, "query", params, GET, ReadAlignment.class);
}
/**
* Samtools is a program for interacting with high-throughput sequencing data in SAM, BAM and CRAM formats. Supported Samtools
* commands: sort, index, view, stats, flagstat, dict, faidx, depth, plot-bamstats.
* @param data Samtools parameters. Supported Samtools commands: sort, index, view, stats, flagstat, dict, faidx, depth, plot-bamstats.
* @param params Map containing any of the following optional parameters.
* study: study.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runSamtools(SamtoolsWrapperParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("analysis", null, "alignment/samtools", null, "run", params, POST, Job.class);
}
}
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