Merge discvr-20.11 to discvr-21.3

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/reference_library_members/.qview.xml

@@ -2,6 +2,7 @@
    <columns>
        <column name="library_id" />
        <column name="ref_nt_id" />
+       <column name="alias" />
        <column name="start" />
        <column name="stop" />
        <column name="type" />

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.324-12.325.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.reference_library_members ADD alias VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.325-12.326.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column codon type VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.326-12.327.sql

@@ -0,0 +1,5 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column ref_aa type VARCHAR(4000);
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column q_aa type VARCHAR(4000);
+
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column ref_nt type VARCHAR(4000);
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column q_nt type VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.324-12.325.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.reference_library_members ADD alias VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.325-12.326.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column codon VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.326-12.327.sql

@@ -0,0 +1,6 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column ref_aa VARCHAR(4000);
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column q_aa VARCHAR(4000);
+
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column ref_nt VARCHAR(4000);
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column q_nt VARCHAR(4000);
+

SequenceAnalysis/resources/schemas/sequenceanalysis.xml

@@ -2234,6 +2234,9 @@
                     <fkColumnName>rowid</fkColumnName>
                 </fk>
             </column>
+            <column columnName="alias">
+                <description>Optional.  Can be used to give the sequence a local name</description>
+            </column>
             <column columnName="start">
                 <description>Optional.  Can be used in conjunction with stop to select a subsequence of the reference.  If blank the region will begin at the first base of the reference</description>
             </column>

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceImportPanel.js

@@ -414,8 +414,9 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
     ILLUMINA_REGEX: /^(.+)_L(.+)_(R){0,1}([0-9])(_[0-9]+){0,1}(\.f(ast){0,1}q)(\.gz)?$/i,
 
     //Example from NextSeq: RNA160915BB_34A_22436_Gag120_Clone-10_S10_R1_001.fastq.gz
+    //OR: 	210304_NS500556_0465_AHHVNKAFX2.OSPHL00042_old_cdna_2.R2.fq.gz
     //This should also allow simple pairs, like: file1_1.fq.gz and file1_2.fq.gz
-    ILLUMINA_REGEX_NO_LANE: /^(.+)_(R){0,1}([0-9])(_[0-9]+){0,1}(\.f(ast){0,1}q)(\.gz)?$/i,
+    ILLUMINA_REGEX_NO_LANE: /^(.+)[\._](R){0,1}([0-9])(_[0-9]+){0,1}(\.f(ast){0,1}q)(\.gz)?$/i,
 
     //example: 214-3-6-GEX_1_S29_L002_R1_001.fastq.gz
     //<sample name>_<barcode sequence>_L<lane (0-padded to 3 digits)>_R<read number>_<set number (0-padded to 3 digits>.fastq.gz

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -94,6 +94,7 @@
 import org.labkey.sequenceanalysis.run.analysis.ImmunoGenotypingAnalysis;
 import org.labkey.sequenceanalysis.run.analysis.LofreqAnalysis;
 import org.labkey.sequenceanalysis.run.analysis.MergeLoFreqVcfHandler;
+import org.labkey.sequenceanalysis.run.analysis.NextCladeHandler;
 import org.labkey.sequenceanalysis.run.analysis.PARalyzerAnalysis;
 import org.labkey.sequenceanalysis.run.analysis.PangolinHandler;
 import org.labkey.sequenceanalysis.run.analysis.PindelAnalysis;
@@ -178,7 +179,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 12.324;
+        return 12.327;
     }
 
     @Override
@@ -349,6 +350,7 @@ public static void registerPipelineSteps()
         SequenceAnalysisService.get().registerFileHandler(new GenomicsDBAppendHandler());
         SequenceAnalysisService.get().registerFileHandler(new MergeLoFreqVcfHandler());
         SequenceAnalysisService.get().registerFileHandler(new PangolinHandler());
+        SequenceAnalysisService.get().registerFileHandler(new NextCladeHandler());
 
         SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());