[med-svn] [Git][med-team/igv][upstream] New upstream version 2.16.2+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Oct 8 17:26:13 BST 2023
Pierre Gruet pushed to branch upstream at Debian Med / igv
Commits:
fc1b1c6d by Pierre Gruet at 2023-10-08T13:54:58+02:00
New upstream version 2.16.2+dfsg
- - - - -
3 changed files:
- src/main/java/org/broad/igv/sam/SAMAlignment.java
- + test/sessions/10x_sc_session.xml
- test/sessions/circview/schatz_paired-end.xml
Changes:
=====================================
src/main/java/org/broad/igv/sam/SAMAlignment.java
=====================================
@@ -330,12 +330,17 @@ public class SAMAlignment implements Alignment {
Object mm = record.hasAttribute("Mm") ? record.getAttribute("Mm") : record.getAttribute("MM");
byte[] ml = (byte[]) (record.hasAttribute("Ml") ? record.getAttribute("Ml") : record.getAttribute("ML"));
- byte[] sequence = record.getReadBases();
- if (mm.toString().length() == 0) { // TODO -- more extensive validation?
- baseModificationSets = Collections.EMPTY_LIST;
- } else {
- baseModificationSets = BaseModificationUtils.getBaseModificationSets(mm.toString(), ml, sequence, isNegativeStrand());
+ // Minimal tag validation
+ if(mm instanceof String && (ml == null || ml instanceof byte [])) {
+
+ byte[] sequence = record.getReadBases();
+
+ if (mm.toString().length() == 0) { // TODO -- more extensive validation?
+ baseModificationSets = Collections.EMPTY_LIST;
+ } else {
+ baseModificationSets = BaseModificationUtils.getBaseModificationSets((String) mm, ml, sequence, isNegativeStrand());
+ }
}
}
return baseModificationSets;
=====================================
test/sessions/10x_sc_session.xml
=====================================
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<Session genome="hg38_1kg" locus="chr3:38368124-38457202" version="8">
+ <Resources>
+ <Resource index="https://cf.10xgenomics.com/samples/cell-exp/7.0.1/SC3pv3_GEX_Human_PBMC/SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam.bai" path="https://cf.10xgenomics.com/samples/cell-exp/7.0.1/SC3pv3_GEX_Human_PBMC/SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam" type="bam"/>
+ </Resources>
+ <Panel height="3212" name="Panel1689308075397" width="1422">
+ <Track attributeKey="SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam Coverage" autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" fontSize="12" id="https://cf.10xgenomics.com/samples/cell-exp/7.0.1/SC3pv3_GEX_Human_PBMC/SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam_coverage" name="SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam Coverage" snpThreshold="0.2" visible="true">
+ <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="17.0" minimum="0.0" type="LINEAR"/>
+ </Track>
+ <Track attributeKey="SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam Junctions" autoScale="false" clazz="org.broad.igv.sam.SpliceJunctionTrack" fontSize="12" groupByStrand="false" height="60" id="https://cf.10xgenomics.com/samples/cell-exp/7.0.1/SC3pv3_GEX_Human_PBMC/SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam_junctions" maxdepth="50" name="SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam Junctions" visible="true"/>
+ <Track attributeKey="SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam" clazz="org.broad.igv.sam.AlignmentTrack" color="185,185,185" displayMode="EXPANDED" experimentType="RNA" fontSize="12" id="https://cf.10xgenomics.com/samples/cell-exp/7.0.1/SC3pv3_GEX_Human_PBMC/SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam" name="SC3pv3_GEX_Human_PBMC_possorted_genome_bam.bam" visible="true">
+ <RenderOptions/>
+ </Track>
+ </Panel>
+ <Panel height="165" name="FeaturePanel" width="1422">
+ <Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="12" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="POSITIVE" shouldShowTranslation="false" visible="true"/>
+ <Track attributeKey="Refseq Genes" clazz="org.broad.igv.track.FeatureTrack" colorScale="ContinuousColorScale;0.0;836.0;255,255,255;0,0,178" fontSize="12" groupByStrand="false" id="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz" name="Refseq Genes" visible="true"/>
+ </Panel>
+ <PanelLayout dividerFractions="0.010550996483001172,0.8007033997655334"/>
+ <HiddenAttributes>
+ <Attribute name="DATA FILE"/>
+ <Attribute name="DATA TYPE"/>
+ <Attribute name="NAME"/>
+ </HiddenAttributes>
+</Session>
=====================================
test/sessions/circview/schatz_paired-end.xml
=====================================
@@ -1,29 +1,26 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<Session genome="hg19" locus="chr17:37276854-37277154" version="8">
+<Session genome="hg19" locus="All" version="8">
<Resources>
+ <Resource path="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam.delly_noalt_filtered.vcf.gz" type="vcf"/>
<Resource path="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam" type="bam"/>
- <Resource path="https://s3.amazonaws.com/igv.org.demo/SKBR3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt_filtered.tra.vcf" type="vcf"/>
</Resources>
- <Panel height="137" name="DataPanel" width="1465">
- <Track attributeKey="reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt_filtered.tra.vcf" clazz="org.broad.igv.variant.VariantTrack" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;0,0,178" displayMode="EXPANDED" fontSize="10" groupByStrand="false" id="https://s3.amazonaws.com/igv.org.demo/SKBR3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt_filtered.tra.vcf" name="reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt_filtered.tra.vcf" siteColorMode="ALLELE_FREQUENCY" visible="true"/>
- </Panel>
- <Panel height="134" name="Panel1643653158403" width="1465">
+ <Panel height="64" name="Panel1643653158403" width="1133">
<Track attributeKey="SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam.delly_noalt_filtered.vcf.gz" clazz="org.broad.igv.variant.VariantTrack" colorScale="ContinuousColorScale;0.0;52.0;255,255,255;0,0,178" displayMode="EXPANDED" fontSize="10" groupByStrand="false" id="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam.delly_noalt_filtered.vcf.gz" name="Delly SVs" siteColorMode="ALLELE_FREQUENCY" squishedHeight="1" visible="true"/>
</Panel>
- <Panel height="2648" name="Panel1643653129901" width="1465">
+ <Panel height="379" name="Panel1643653129901" width="1133">
<Track attributeKey="SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam Coverage" autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" fontSize="10" id="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam_coverage" name="Illumina Coverage" snpThreshold="0.2" visible="true">
- <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="180.0" minimum="0.0" type="LINEAR"/>
+ <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="17.761848" minimum="0.0" type="LINEAR"/>
</Track>
- <Track attributeKey="SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam Junctions" autoScale="false" clazz="org.broad.igv.sam.SpliceJunctionTrack" fontSize="10" groupByStrand="false" height="60" id="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam_junctions" maxdepth="50" name="Illumina Junctions" visible="false"/>
+ <Track attributeKey="SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam Junctions" clazz="org.broad.igv.sam.SpliceJunctionTrack" fontSize="10" groupByStrand="false" height="60" id="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam_junctions" name="Illumina Junctions" visible="false"/>
<Track attributeKey="SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam" clazz="org.broad.igv.sam.AlignmentTrack" color="185,185,185" displayMode="EXPANDED" experimentType="OTHER" fontSize="10" id="https://s3.amazonaws.com/igv.org.demo/SKBR3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam" name="Illumina Alignments" visible="true">
<RenderOptions/>
</Track>
</Panel>
- <Panel height="136" name="FeaturePanel" width="1465">
+ <Panel height="96" name="FeaturePanel" width="1133">
<Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="POSITIVE" shouldShowTranslation="true" visible="true"/>
<Track attributeKey="Refseq Genes" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" groupByStrand="false" id="https://s3.amazonaws.com/igv.org.genomes/hg19/ncbiRefSeq.sorted.txt.gz" name="Refseq Genes" visible="true"/>
</Panel>
- <PanelLayout dividerFractions="0.18051948051948052,0.36103896103896105,0.8168831168831169"/>
+ <PanelLayout dividerFractions="0.010714285714285714,0.13392857142857142,0.8196428571428571"/>
<HiddenAttributes>
<Attribute name="DATA FILE"/>
<Attribute name="DATA TYPE"/>
View it on GitLab: https://salsa.debian.org/med-team/igv/-/commit/fc1b1c6df3b8d5647908464574bf3c3fea24cdcb
--
View it on GitLab: https://salsa.debian.org/med-team/igv/-/commit/fc1b1c6df3b8d5647908464574bf3c3fea24cdcb
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20231008/d94ae512/attachment-0001.htm>
More information about the debian-med-commit
mailing list