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.
type
String. Conditional.
If the type parameter is not provided, name is considered as analysis name, For sample name(s), type is mandatory (For example, type=sample).
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Sample request
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https://ionreporter.thermofisher.com/api/v1/getAssociatedBamfiles?name=multi
bam test,Sample_1_v2,test62,1194954B_Bladder_ManLib,Demo AmpliSeq
Exome VCF,invalid_sapmle1,Demo AmpliSeq IDP
Mother&type=sample
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Analysis request
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http://ionreporter.thermofisher.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://ionreporter.thermofisher.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://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/Zyklus/data/IRU_Uploads/2017-12-29_1_51_48/v1/e5272-wfa-l165_v3/rawlib.bam",
"http://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/Zyklus/data/IRU_Uploads/20171229_14_54_21/v1/sample_test16/1_IonDx-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://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_daughter.bam"
],
"processedBam": [
"http://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/uattestsskadmuser@gmail.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://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_father.bam"
],
"processedBam": [
"http://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/uattestsskadmuser@gmail.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://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_mother.bam"
],
"processedBam": [
"http://ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/uattestsskadmuser@gmail.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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