From 3d18f3af76bcd08ba763add51ce9ef7206381f04 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 26 Dec 2025 06:57:44 -0800
Subject: [PATCH 1/3] Bugfix to mGAP download window

---
 mGAP/resources/web/mGAP/DownloadWindow.js | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/mGAP/resources/web/mGAP/DownloadWindow.js b/mGAP/resources/web/mGAP/DownloadWindow.js
index f18dffef..fde3f1b1 100644
--- a/mGAP/resources/web/mGAP/DownloadWindow.js
+++ b/mGAP/resources/web/mGAP/DownloadWindow.js
@@ -54,9 +54,10 @@ Ext4.define('mGAP.window.DownloadWindow', {
 
                 LDK.Assert.assertNotEmpty('Missing objectId variantCatalogReleases', results.rows[0].objectId);
 
-                var releaseVcf = results.rows[0].objectId + '/' + results.rows[0]['vcfId/dataid/Name'];
-                var urlFasta = results.rows[0]['vcfId/library_id/fasta_file/Name'];
-                var sitesOnlyVcf = results.rows[0].objectId + '/' + results.rows[0]['sitesOnlyVcfId/dataid/Name'];
+                var releaseVcfWithGUID = results.rows[0].objectId + '/' + results.rows[0]['vcfId/dataid/Name'];
+                var sitesOnlyVcfWithGUID = results.rows[0].objectId + '/' + results.rows[0]['sitesOnlyVcfId/dataid/Name'];
+                var genomeFasta = results.rows[0]['vcfId/library_id/fasta_file/Name'];
+                var genomeDict = genomeFasta.replace(/fasta$/, 'dict')
 
                 const getFileName = function(path){
                     path = path.split('/');
@@ -66,16 +67,16 @@ Ext4.define('mGAP.window.DownloadWindow', {
                 var toAdd = [{
                     html: 'Due to the large file size, the preferred option is to download using wget or curl on the command line, such as the exmaples below. Nonetheless, you also are able to paste the URLs into your browser and download through this way as well, although it will be slower and possibly not able to resume if your connection is disrupted.<br><br>' +
                             'Use these to download the VCF and index. Note, -C will allow file resume if the download is disrupted:<br>' +
-                            '<pre>curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + releaseVcf + '<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + releaseVcf + '.tbi</pre>' +
-                            (sitesOnlyVcf ?
+                            '<pre>curl -C - -o ' + getFileName(releaseVcfWithGUID) + ' https://mgapdownload.ohsu.edu/' + releaseVcfWithGUID + '<br>' +
+                            'curl -C - -o ' + getFileName(releaseVcfWithGUID) + '.tbi' + ' https://mgapdownload.ohsu.edu/' + releaseVcfWithGUID + '.tbi</pre>' +
+                            (sitesOnlyVcfWithGUID ?
                             'or a VCF without genotypes (considerably smaller):<br>' +
-                            '<pre>curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '.tbi</pre>' : '') +
+                            '<pre>curl -C - -o ' + getFileName(sitesOnlyVcfWithGUID) + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcfWithGUID + '<br>' +
+                            'curl -C - -o ' + getFileName(sitesOnlyVcfWithGUID) + '.tbi' + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcfWithGUID + '.tbi</pre>' : '') +
                             'and genome:<br>' +
-                            '<pre>curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '.fai<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/genomes/' + urlFasta.replace(/fasta$/, 'dict') + '</pre>'
+                            '<pre>curl -C - -o ' + getFileName(genomeFasta) + ' https://mgapdownload.ohsu.edu/genomes/' + genomeFasta + '<br>' +
+                            'curl -C - -o ' + getFileName(genomeFasta) + '.fai' + ' https://mgapdownload.ohsu.edu/genomes/' + genomeFasta + '.fai<br>' +
+                            'curl -C - -o ' + getFileName(genomeDict) + ' https://mgapdownload.ohsu.edu/genomes/' + genomeDict + '</pre>'
                 },{
                     html: '<br><b>mGAP is an NIH funded project.  If you use these data in a publication, we ask that you please include R24 OD021324 in the acknowledgements.</b>',
                     border: false,

From 5f6e5e01f75ea66c76537c8c3c30036f89458d29 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 29 Dec 2025 16:15:10 -0800
Subject: [PATCH 2/3] Improve resource check

---
 .../primeseq/pipeline/SequenceJobResourceAllocator.java     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java
index b7bfe56d..8f57b6ae 100644
--- a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java
+++ b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java
@@ -69,9 +69,9 @@ private boolean isSequenceAlignmentTask(PipelineJob job)
         return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("SequenceAlignmentTask"));
     }
 
-    private boolean isCacheAlignerIndexesTask(PipelineJob job)
+    private boolean isCacheOrPrepareAlignerIndexesTask(PipelineJob job)
     {
-        return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("CacheAlignerIndexesTask"));
+        return (job.getActiveTaskId() != null && (job.getActiveTaskId().getNamespaceClass().getName().endsWith("CacheAlignerIndexesTask") || job.getActiveTaskId().getNamespaceClass().getName().endsWith("PrepareAlignerIndexesTask")));
     }
 
     private boolean isSequenceSequenceOutputHandlerTask(PipelineJob job)
@@ -188,7 +188,7 @@ public Integer getMaxRequestMemory(PipelineJob job)
             return 96;
         }
 
-        if (isCacheAlignerIndexesTask(job))
+        if (isCacheOrPrepareAlignerIndexesTask(job))
         {
             int mem = getAlignerIndexMem(job);
             job.getLogger().debug("setting memory to: " + mem);

From adfca6696f8c36a9abf0fa6441584e19a6c453fa Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 31 Dec 2025 08:43:48 -0800
Subject: [PATCH 3/3] Support more clonotype filters

---
 tcrdb/resources/schemas/tcrdb.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tcrdb/resources/schemas/tcrdb.xml b/tcrdb/resources/schemas/tcrdb.xml
index a8a486ce..34d61439 100644
--- a/tcrdb/resources/schemas/tcrdb.xml
+++ b/tcrdb/resources/schemas/tcrdb.xml
@@ -129,7 +129,7 @@
                 <columnTitle>Clonotype</columnTitle>
             </column>
             <column columnName="activationFrequency">
-                <columnTitle>Activated Freq</columnTitle>
+                <columnTitle>Activated Freq (of parent population)</columnTitle>
             </column>
             <column columnName="backgroundFrequency">
                 <columnTitle>Background Freq</columnTitle>