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URL
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/api/v1/getAssociatedBamfiles
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Description
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For use with the Ion Reporter™ Server only. Gets the BAM file or files that are associated with a single sample or analysis, or multiple samples or analyses, and downloads the BAM files using the /downloadBAM API call. Returns a JSON response object that contains the BAM file links. After BAM files are displayed as output as JSON, users can download the BAM file using the /api/v1/downloadBAM API call.
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Method
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GET
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Request query parameters
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-
name
String, Mandatory.
Single/multiple names of either sample or analysis.
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type
String. Conditional.
Valid values are "sample" or "analysis".
If the type parameter is not provided, "analysis" is used as the default value.
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Sample request
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https://user1.XYZ.com/api/v1/getAssociatedBamfiles?name=multi
bam test,Sample_1_v2,test62,1194954B_Bladder_ManLib,Demo%AmpliSeq
Exome VCF,invalid_samp1e,Demo AmpliSeq IDP
Mother&type=sample
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Analysis request
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http://user1.XYZ.com/api/v1/getAssociatedBamfiles?name=Demo
AmpliSeq IDP
Daughter_1518065163079,invalid_name,trio_c1078_2018-03-01-20-35-30-948
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Request headers
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Content-Type: application/x-www-form-urlencoded
Authorization:API Token
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Returns
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Sample Response [
{
"sample": "1194954B_Bladder_ManLib",
"bam_links": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/
Zyklus/data/IRU_Uploads/20170727_08_45_03/v1/1194954B_Bladder_ManLib/1_IonXpress_030_R_2016_12_20_13_27_19_user_S5-00105-348-C656s2_OCAv3.4_CNVbaseline_ManLibs_Pool6_chip6_Auto_user_S5-00105-348-C656s2_OCAv3.4_CNVbaseline_ManLibs_Pool6_chip6_1074.bam"
]
},
{
"sample": "invalid_sapmle1",
"bam_links": [
"Sample or Bam file could not be found for the specified name."
]
},
{
"sample": "multi bam test",
"bam_links": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ/data/IRU_Uploads/2017-12-29_1_51_48/v1/e5272-wfa-l165_v3/rawlib.bam",
"http://user1.XYZ.com.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ/data/IRU_Uploads/20171229_14_54_21/v1/sample_test16/1_I-9_rawlib12.bam"
]
},
{
"sample": "Demo AmpliSeq Exome VCF",
"bam_links": [
"Sample or Bam file could not be found for the specified name."
]
}
]
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Analysis Response
[
{
"analysis": "trio_c1078_2018-03-01-20-35-30-948",
"version": "IR510",
"analysisStatus": "SUCCESSFUL",
"sampleDetails": [
{
"sampleName": "Demo AmpliSeq IDP Daughter",
"sampleRole": "proband",
"inputBam": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_daughter.bam"
],
"processedBam": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ-Labs/user1@XYZ.com/Demo_AmpliSeq_IDP_Daughter_Demo_AmpliSeq_IDP_Father_Demo_AmpliSeq_IDP_Mother/Demo_AmpliSeq_IDP_Daughter_20180301150555171/outputs/VariantCallerActorProband-00/merged.bam.ptrim.bam"
]
},
{
"sampleName": "Demo AmpliSeq IDP Father",
"sampleRole": "father",
"inputBam": [
"http://user1.XYZ.com.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_father.bam"
],
"processedBam": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ-Labs/user1@XYZ.com/Demo_AmpliSeq_IDP_Daughter_Demo_AmpliSeq_IDP_Father_Demo_AmpliSeq_IDP_Mother/Demo_AmpliSeq_IDP_Daughter_20180301150555171/outputs/VariantCallerActorFather-00/merged.bam.ptrim.bam"
]
},
{
"sampleName": "Demo AmpliSeq IDP Mother",
"sampleRole": "mother",
"inputBam": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_mother.bam"
],
"processedBam": [
"http://user1.XYZ.com:80/api/v1/downloadBAM?filePath=/shared/data/XYZ-Labs/user1@XYZ.com/Demo_AmpliSeq_IDP_Daughter_Demo_AmpliSeq_IDP_Father_Demo_AmpliSeq_IDP_Mother/Demo_AmpliSeq_IDP_Daughter_20180301150555171/outputs/VariantCallerActorMother-00/merged.bam.ptrim.bam"
]
}
]
},
{
"analysis": "invalid_name",
"message": "Analysis could not be found for the specified name."
}
]
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