Updated docs
diff --git a/docs/dyn/genomics_v1beta2.readgroupsets.html b/docs/dyn/genomics_v1beta2.readgroupsets.html
index c52c1fd..098920f 100644
--- a/docs/dyn/genomics_v1beta2.readgroupsets.html
+++ b/docs/dyn/genomics_v1beta2.readgroupsets.html
@@ -80,12 +80,6 @@
<p class="firstline">Returns the coveragebuckets Resource.</p>
<p class="toc_element">
- <code><a href="#align">align(body)</a></code></p>
-<p class="firstline">Aligns read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.</p>
-<p class="toc_element">
- <code><a href="#call">call(body)</a></code></p>
-<p class="firstline">Calls variants on read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.</p>
-<p class="toc_element">
<code><a href="#delete">delete(readGroupSetId)</a></code></p>
<p class="firstline">Deletes a read group set.</p>
<p class="toc_element">
@@ -108,83 +102,6 @@
<p class="firstline">Updates a read group set.</p>
<h3>Method Details</h3>
<div class="method">
- <code class="details" id="align">align(body)</code>
- <pre>Aligns read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.
-
-Args:
- body: object, The request body. (required)
- The object takes the form of:
-
-{ # The read group set align request.
- "interleavedFastqSource": { # Describes an interleaved FASTQ file source for alignment. # The interleaved FASTQ source files for alignment, where both members of each pair of reads are found on consecutive records within the same FASTQ file. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.
- "sourceUris": [ # A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage which will be aligned. The caller must have READ permissions for these files.
- "A String",
- ],
- "metadata": { # Optionally specifies the metadata to be associated with the final aligned read group set.
- "readGroupName": "A String", # Optionally specifies the read group name for alignment from FASTQ.
- "sampleName": "A String", # Optionally specifies the sample name for alignment from FASTQ.
- "libraryName": "A String", # Optionally specifies the library name for alignment from FASTQ.
- "platformName": "A String", # Optionally specifies the platform name for alignment from FASTQ. For example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
- "platformUnit": "A String", # Optionally specifies the platform unit for alignment from FASTQ. For example: flowcell-barcode.lane for Illumina or slide for SOLID.
- },
- },
- "bamSourceUris": [ # The BAM source files for alignment. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided. The caller must have READ permissions for these files.
- "A String",
- ],
- "pairedFastqSource": { # Describes a paired-end FASTQ file source for alignment. # The paired end FASTQ source files for alignment, where each member of a pair of reads are found in separate files. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.
- "secondSourceUris": [ # A list of URIs pointing at paired end FASTQ files in Google Cloud Storage which will be aligned. The second of each paired file should be specified here, in an order that matches the first of each paired file specified in firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ permissions for these files.
- "A String",
- ],
- "metadata": { # Optionally specifies the metadata to be associated with the final aligned read group set.
- "readGroupName": "A String", # Optionally specifies the read group name for alignment from FASTQ.
- "sampleName": "A String", # Optionally specifies the sample name for alignment from FASTQ.
- "libraryName": "A String", # Optionally specifies the library name for alignment from FASTQ.
- "platformName": "A String", # Optionally specifies the platform name for alignment from FASTQ. For example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
- "platformUnit": "A String", # Optionally specifies the platform unit for alignment from FASTQ. For example: flowcell-barcode.lane for Illumina or slide for SOLID.
- },
- "firstSourceUris": [ # A list of URIs pointing at paired end FASTQ files in Google Cloud Storage which will be aligned. The first of each paired file should be specified here, in an order that matches the second of each paired file specified in secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ permissions for these files.
- "A String",
- ],
- },
- "readGroupSetId": "A String", # The ID of the read group set which will be aligned. A new read group set will be generated to hold the aligned data, the originals will not be modified. The caller must have READ permissions for this read group set. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.
- "datasetId": "A String", # Required. The ID of the dataset the newly aligned read group sets will belong to. The caller must have WRITE permissions to this dataset.
- }
-
-
-Returns:
- An object of the form:
-
- { # The read group set align response.
- "jobId": "A String", # A job ID that can be used to get status information.
- }</pre>
-</div>
-
-<div class="method">
- <code class="details" id="call">call(body)</code>
- <pre>Calls variants on read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.
-
-Args:
- body: object, The request body. (required)
- The object takes the form of:
-
-{ # The read group set call request.
- "sourceUris": [ # A list of URIs pointing at BAM files in Google Cloud Storage which will be called. FASTQ files are not allowed. The caller must have READ permissions for these files. One of readGroupSetId or sourceUris must be provided.
- "A String",
- ],
- "readGroupSetId": "A String", # The IDs of the read group sets which will be called. The caller must have READ permissions for these read group sets. One of readGroupSetId or sourceUris must be provided.
- "datasetId": "A String", # Required. The ID of the dataset the called variants will belong to. The caller must have WRITE permissions to this dataset.
- }
-
-
-Returns:
- An object of the form:
-
- { # The read group set call response.
- "jobId": "A String", # A job ID that can be used to get status information.
- }</pre>
-</div>
-
-<div class="method">
<code class="details" id="delete">delete(readGroupSetId)</code>
<pre>Deletes a read group set.
@@ -208,10 +125,10 @@
"referenceNames": [ # The reference names to export. If this is not specified, all reference sequences, including unmapped reads, are exported. Use * to export only unmapped reads.
"A String",
],
- "readGroupSetIds": [ # Required. The IDs of the read group sets to export.
+ "readGroupSetIds": [ # Required. The IDs of the read group sets to export. The caller must have READ access to these read group sets.
"A String",
],
- "projectNumber": "A String", # Required. The Google Developers Console project number that owns this export.
+ "projectNumber": "A String", # Required. The Google Developers Console project number that owns this export. The caller must have WRITE access to this project.
}
@@ -258,7 +175,7 @@
"prevProgramId": "A String", # The ID of the program run before this one.
"id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
"version": "A String", # The version of the program run.
- "name": "A String", # The name of the program.
+ "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
},
],
"sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
@@ -268,7 +185,7 @@
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
"platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
},
- "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. Required if there are any read alignments.
+ "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
"id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
"datasetId": "A String", # The ID of the dataset this read group belongs to.
"description": "A String", # A free-form text description of this read group.
@@ -289,7 +206,7 @@
- Tags will be converted to strings - tag types are not preserved
- Comments (@CO) in the input file header are not imported
- Original order of reference headers is not preserved
-- Any reverse stranded unmapped reads will be reverse complemented, and their qualities (and "BQ" tag, if any) will be reversed
+- Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
- Unmapped reads will be stripped of positional information (referenceName and position)
Args:
@@ -348,7 +265,7 @@
"prevProgramId": "A String", # The ID of the program run before this one.
"id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
"version": "A String", # The version of the program run.
- "name": "A String", # The name of the program.
+ "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
},
],
"sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
@@ -358,7 +275,7 @@
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
"platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
},
- "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. Required if there are any read alignments.
+ "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
"id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
"datasetId": "A String", # The ID of the dataset this read group belongs to.
"description": "A String", # A free-form text description of this read group.
@@ -399,7 +316,7 @@
"prevProgramId": "A String", # The ID of the program run before this one.
"id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
"version": "A String", # The version of the program run.
- "name": "A String", # The name of the program.
+ "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
},
],
"sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
@@ -409,7 +326,7 @@
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
"platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
},
- "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. Required if there are any read alignments.
+ "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
"id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
"datasetId": "A String", # The ID of the dataset this read group belongs to.
"description": "A String", # A free-form text description of this read group.
@@ -438,7 +355,7 @@
"A String",
],
"name": "A String", # Only return read group sets for which a substring of the name matches this string.
- "pageSize": 42, # Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 1024.
+ "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, defaults to 256. The maximum value is 1024.
}
@@ -473,7 +390,7 @@
"prevProgramId": "A String", # The ID of the program run before this one.
"id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
"version": "A String", # The version of the program run.
- "name": "A String", # The name of the program.
+ "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
},
],
"sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
@@ -483,7 +400,7 @@
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
"platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
},
- "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. Required if there are any read alignments.
+ "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
"id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
"datasetId": "A String", # The ID of the dataset this read group belongs to.
"description": "A String", # A free-form text description of this read group.
@@ -532,7 +449,7 @@
"prevProgramId": "A String", # The ID of the program run before this one.
"id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
"version": "A String", # The version of the program run.
- "name": "A String", # The name of the program.
+ "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
},
],
"sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
@@ -542,7 +459,7 @@
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
"platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
},
- "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. Required if there are any read alignments.
+ "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
"id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
"datasetId": "A String", # The ID of the dataset this read group belongs to.
"description": "A String", # A free-form text description of this read group.
@@ -583,7 +500,7 @@
"prevProgramId": "A String", # The ID of the program run before this one.
"id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
"version": "A String", # The version of the program run.
- "name": "A String", # The name of the program.
+ "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
},
],
"sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
@@ -593,7 +510,7 @@
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
"platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
},
- "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. Required if there are any read alignments.
+ "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
"id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
"datasetId": "A String", # The ID of the dataset this read group belongs to.
"description": "A String", # A free-form text description of this read group.