From 000b5ba60c5fb6cddfd56eb19dcaecebde549d1e Mon Sep 17 00:00:00 2001
From: Michael Baudis <mbaudis@me.com>
Date: Thu, 25 Jul 2024 13:50:28 +0900
Subject: [PATCH] mateStart etc

---
 src/config/beaconSearchParameters.yaml | 76 +++++++++++++++++++++++++-
 1 file changed, 75 insertions(+), 1 deletion(-)

diff --git a/src/config/beaconSearchParameters.yaml b/src/config/beaconSearchParameters.yaml
index 38302b84..520eb4e3 100644
--- a/src/config/beaconSearchParameters.yaml
+++ b/src/config/beaconSearchParameters.yaml
@@ -5,11 +5,13 @@ parameters:
     defaultValue: ["progenetix"]
     options:
       - value: progenetix
-        label: Progenetix
+        label: Progenetix cancer genome variants
       - value: cellz
         label: Cancer Cell Lines Collection
       - value: examplez
         label: Test Database - examplez
+      - value: refcnv
+        label: refCNV - germline reference CNVs
     isMulti: true
   assemblyId:
     label: Genome Assembly
@@ -88,6 +90,60 @@ parameters:
         value: "refseq:NC_000023.11"
       - label: "Y (NC_000024.10)"
         value: "refseq:NC_000024.10"
+  mateName:
+    label: Fusion Chromosome
+    infoText: The second chromosome in a fusion (transmitted as refseq id).
+    options:
+      - label: "(none)"
+        value: ""
+      - label: "1 (NC_000001.11)"
+        value: "refseq:NC_0000001.11"
+      - label: "2 (NC_000002.12)"
+        value: "refseq:NC_000002.12"
+      - label: "3 (NC_000003.12)"
+        value: "refseq:NC_000003.12"
+      - label: "4 (NC_000004.12)"
+        value: "refseq:NC_000004.12"
+      - label: "5 (NC_000005.10)"
+        value: "refseq:NC_000005.10"
+      - label: "6 (NC_000006.12)"
+        value: "refseq:NC_000006.12"
+      - label: "7 (NC_000007.14)"
+        value: "refseq:NC_000007.14"
+      - label: "8 (NC_000008.11)"
+        value: "refseq:NC_000008.11"
+      - label: "9 (NC_000009.12)"
+        value: "refseq:NC_000009.12"
+      - label: "10 (NC_000010.11)"
+        value: "refseq:NC_000010.11"
+      - label: "11 (NC_000011.10)"
+        value: "refseq:NC_000011.10"
+      - label: "12 (NC_000012.12)"
+        value: "refseq:NC_000012.12"
+      - label: "13 (NC_000013.11)"
+        value: "refseq:NC_000013.11"
+      - label: "14 (NC_000014.9)"
+        value: "refseq:NC_000014.9"
+      - label: "15 (NC_000015.10)"
+        value: "refseq:NC_000015.10"
+      - label: "16 (NC_000016.10)"
+        value: "refseq:NC_000016.10"
+      - label: "17 (NC_000017.11)"
+        value: "refseq:NC_000017.11"
+      - label: "18 (NC_000018.10)"
+        value: "refseq:NC_000018.10"
+      - label: "19 (NC_000019.10)"
+        value: "refseq:NC_000019.10"
+      - label: "20 (NC_000020.11)"
+        value: "refseq:NC_000020.11"
+      - label: "21 (NC_000021.9)"
+        value: "refseq:NC_000021.9"
+      - label: "22 (NC_000022.11)"
+        value: "refseq:NC_000022.11"
+      - label: "X (NC_000023.11)"
+        value: "refseq:NC_000023.11"
+      - label: "Y (NC_000024.10)"
+        value: "refseq:NC_000024.10"
   variantType:
     label: "Variant Type"
     infoText: >-
@@ -108,6 +164,10 @@ parameters:
         label: "EFO:0030066 (any relative CN variation)"
       - value: "SO:0001059"
         label: "SO:0001059 (any sequence alteration - SNV, INDEL...)"
+      - value: "SO:0000806"
+        label: "SO:0000806 (fusion)"
+      - value: "SO:0001413"
+        label: "SO:0001413 (translocation breakpoint)"
   start:
     label: Start or Position
     placeholder: "19000001-21975098"
@@ -125,6 +185,20 @@ parameters:
       single value, or in case of fuzzy requests for e.g. copy number variants
       the end provided as a range for the possible occurrence of
       the CNV end (e.g. "21967753-22500000").
+  mateStart:
+    label: Mate Start
+    placeholder: "23000000"
+    infoText: |
+      The (1-based) stat of genomic position of the range in which the fusion partners
+      breakpoint position should fall. In contrast to the general "start" parameter
+      only a single value can be used.
+  mateEnd:
+    label: Mate End
+    placeholder: "23000000"
+    infoText: |
+      The (1-based) stat of genomic position of the range in which the fusion partners
+      breakpoint position should fall. In contrast to the general "end" parameter
+      only a single value can be used.
   cytoBands:
     label: Cytoband Annotation
     type: string