From 224f360c5ffc8a059df88fcfb69be47661598d73 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 14 Jan 2026 21:50:54 -0800 Subject: [PATCH 1/2] Bugfix to barcode inclusion list --- .../src/org/labkey/singlecell/run/CellRangerGexCountStep.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java index 35a2083a5..8c89f82e5 100644 --- a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java +++ b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java @@ -626,7 +626,8 @@ public enum Chemistry // cellranger-x.y.z/lib/python/cellranger/barcodes/ FivePE_V3("Single Cell 5' PE v3", "3M-5pgex-jan-2023.txt.gz"), FivePE_V2("Single Cell 5' PE v2", "737k-august-2016.txt"), - FivePE_V1("Single Cell 5' PE", "737K-april-2014_rc.txt"); + FivePE_V1("Single Cell 5' PE", "737k-august-2016.txt"); + // Single Cell 3' v1: 737K-april-2014_rc.txt final String _label; final String _inclusionListFile; From 914ec467a350d16d875a0ef1ea58e9d67204b36a Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 15 Jan 2026 10:18:40 -0800 Subject: [PATCH 2/2] AUTO_DROP not supported prior to MSSql 2022 --- .../SequenceAnalysis-12.329-12.330.sql | 20 +++++++------------ 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql index 73397ec1d..a358c05e3 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql @@ -17,23 +17,17 @@ CREATE NONCLUSTERED INDEX IDX_alignment_summary_analysis_id_rowid_container_tota rowid ASC, container ASC ) -INCLUDE(total) +INCLUDE(total); -CREATE STATISTICS STAT_ref_nt_sequence_rowid_locus_container ON sequenceanalysis.ref_nt_sequences (RowId, locus, container) -WITH AUTO_DROP = OFF +CREATE STATISTICS STAT_ref_nt_sequence_rowid_locus_container ON sequenceanalysis.ref_nt_sequences (RowId, locus, container); -CREATE STATISTICS STAT_ref_nt_sequence_locus_container ON sequenceanalysis.ref_nt_sequences (locus, container) -WITH AUTO_DROP = OFF +CREATE STATISTICS STAT_ref_nt_sequence_locus_container ON sequenceanalysis.ref_nt_sequences (locus, container); -CREATE STATISTICS STAT_sequence_analyses_container_readset ON sequenceanalysis.sequence_analyses (Container, readset) -WITH AUTO_DROP = OFF +CREATE STATISTICS STAT_sequence_analyses_container_readset ON sequenceanalysis.sequence_analyses (Container, readset); -CREATE STATISTICS STAT_sequence_readsets_rowid_container ON sequenceanalysis.sequence_readsets (RowId, Container) -WITH AUTO_DROP = OFF +CREATE STATISTICS STAT_sequence_readsets_rowid_container ON sequenceanalysis.sequence_readsets (RowId, Container); -CREATE STATISTICS STAT_asj_alignmentid_container_ref_nt_id ON sequenceanalysis.alignment_summary_junction (alignment_id, container, ref_nt_id) -WITH AUTO_DROP = OFF +CREATE STATISTICS STAT_asj_alignmentid_container_ref_nt_id ON sequenceanalysis.alignment_summary_junction (alignment_id, container, ref_nt_id); -CREATE STATISTICS STAT_asj_alignmentid_ref_nt_id_status_alignment_id ON sequenceanalysis.alignment_summary_junction (ref_nt_id, status, alignment_id) -WITH AUTO_DROP = OFF +CREATE STATISTICS STAT_asj_alignmentid_ref_nt_id_status_alignment_id ON sequenceanalysis.alignment_summary_junction (ref_nt_id, status, alignment_id);