Merge branch 'master' of https://gitlab.isb-sib.ch/ST/ga4gh-arraymap

app/node-app/public/pages/doc.md

 ## Current implementation
 
+This beacon queries 20K samples coming from ArrayMap from here:
+http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata
+
 <img src="/img/current_implementation.jpg" class="img-thumbnail img-responsive">
 
 **Comments**
 
-* reference genome: In [In Beacon 0.2 specifications](https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit), the values expected for human data is of GRCh? format, whereas arrayMap uses HG nomenclature.
+* reference genome: In [In Beacon 0.2 specifications](https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit), the values expected for human data is of GRCh format, whereas arrayMap uses HG nomenclature. A mapping 1:1 is done on the fly to convert from GRCh to HG.
 * allele: [In Beacon 0.2 specifications](https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit), the parameter is required. However, it does not make sense at all for arrayMap (in which no sequence related data exists).
 * variantClass: This is a new parameter. The value equals DUP corresponds to SEGTYPE=1 (gain) in arrayMap, while DEL is for SEGTYPE=-1 (loss). The parameter is mandatory.
 * sampleuid: This is DEBUG info.
 * matchedSegment: This is DEBUG info.
+* NOT_BEACON_totalInDataSet: This is also debug info but could be nice to include it as well on Beacon
 
 **Example**
 
-Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a deletion: [query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL](http://beacon-arraymap.vital-it.ch/v0.2/query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL)
+Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a deletion: [query?chromosome=11&position=34439881&reference=GRCh38&dataset=8070/3&variantClass=DEL](http://beacon-arraymap.vital-it.ch/v0.2/query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL)
 
 
 **Outcome from the meeting with Jordi (Feb, 10, 2016):**
@@ -230,3 +234,4 @@ Open questions:
    3. ask the Beacon team if they can make this optional property.
    4. ask the Beacon team if they can replace the property type by a list of strings (instead of a string).
    5. clarify CIPOS and CIEND in VCF v4.2 for DUP/DEL (i.e. CIPOS=-500,500;CIEND=-500,500)
+     - currently, we belief that this is a range, e.g. +/- 500 for POS and END
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