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Merged
bbimber merged 3 commits into from
Jan 15, 2026
Merged

Merge discvr-25.11 to develop #410

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224f360
Bugfix to barcode inclusion list
bbimber Jan 15, 2026
914ec46
AUTO_DROP not supported prior to MSSql 2022
bbimber Jan 15, 2026
39331d1
Merge discvr-25.11 to develop
bbimber Jan 15, 2026
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20 changes: 7 additions & 13 deletions SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -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);

3 changes: 2 additions & 1 deletion singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
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Expand Up @@ -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;
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