# HG changeset patch
# User iuc
# Date 1658921084 0
# Node ID a24ca22b906e5cb6cb40a93d5a12ecbe0f3878c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
diff -r 000000000000 -r a24ca22b906e arriba.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/arriba.xml Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,757 @@
+
+ detect gene fusions from STAR aligned RNA-Seq data
+
+ macros.xml
+
+
+
+
+
+
+ ([AN]C_([*]|\d+))
+ ((chr)?(\d|\d\d|X|Y|M(t)?))
+
+
+
+ Aligned.sortedByCoord.out.bam
+ && samtools index Aligned.sortedByCoord.out.bam
+#end if
+#if $output_fusions_vcf
+ && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf
+#end if
+#if $output_fusion_bams
+ && mkdir fusion_bams
+ && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion'
+#end if
+#if str($visualization.do_viz) == "yes"
+ #set $fusions = 'fusions.tsv'
+ && @DRAW_FUSIONS@
+#end if
+ ]]>
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+ Commma or SPACE separated list, default: gene_name=gene_name|gene_id gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS
+ ^(gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=\w+(|\w+)?([ ,](gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=\w+(|\w+)?)*$
+
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+ When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities.
+
+
+
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+
+
+ Comma-/space-separated list of interesting contigs.
+ Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix "chr".
+ Asterisks (*) are treated as wild-cards.
+ Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*
+
+ ^((@GENOME_CONTIG@|@VIRAL_CONTIG@)([,\s]\s*(*@GENOME_CONTIG@|@VIRAL_CONTIG@))*)*
+
+
+ Comma-/space-separated list of viral contigs for reporting of viral integration sites.
+ Asterisks (*) are treated as wild-cards.
+ Default: AC_* NC_*
+
+ ^(@VIRAL_CONTIG@([,\s]\s*@VIRAL_CONTIG@)*)*$
+
+
+ By default all filters are enabled.
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+ Arriba estimates the number of fusions with a given number of supporting
+ reads which one would expect to see by random chance. If the expected number
+ of fusions (e-value) is higher than this threshold, the fusion is
+ discarded by the 'relative_support' filter. Note: Increasing this
+ threshold can dramatically increase the number of false positives and may
+ increase the runtime of resource-intensive steps. Fractional values are possible.
+ Default: 0.300000
+
+
+
+
+ discard all fusions with fewer than this many supporting reads (split reads and discordant mates combined).
+ Default: 2
+
+
+
+ When more than this fraction of supporting reads turns out to be mismappers,
+ the 'mismappers' filter discards the fusion.
+ Default: 0.800000
+
+
+
+ Genes with more than the given fraction of sequence identity are
+ considered homologs and removed by the 'homologs' filter.
+ Default: 0.300000
+
+
+
+ The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more.
+ Default: 6
+
+
+
+ The 'read_through' filter removes read-through fusions
+ where the breakpoints are less than the given distance away from each other.
+ Default: 10000
+
+
+
+ Alignment artifacts are often characterized by split reads coming
+ from only one gene and no discordant mates. Moreover, the split
+ reads only align to a short stretch in one of the genes. The
+ 'short_anchor' filter removes these fusions. This parameter sets
+ the threshold in bp for what the filter considers short.
+ Default: 23
+
+
+
+ The 'many_spliced' filter recovers fusions between genes that
+ have at least this many spliced breakpoints.
+ Default: 4
+
+
+
+ The 'low_entropy' filter removes reads with repetitive 3-mers. If
+ the 3-mers make up more than the given fraction of the sequence, then
+ the read is discarded.
+ Default: 0.600000
+
+
+
+
+ The 'mismatches' filter uses a binomial model to calculate a
+ p-value for observing a given number of mismatches in a read.
+ If the number of mismatches is too high, the read is discarded.
+ Default: 0.010000
+
+
+
+
+ When paired-end data is given, the fragment length is estimated
+ automatically and this parameter has no effect. But when single-end
+ data is given, the mean fragment length should be specified to
+ effectively filter fusions that arise from hairpin structures.
+ Default: 200
+
+
+
+ Subsample fusions with more than the given number of supporting reads. This
+ improves performance without compromising sensitivity, as long as the
+ threshold is high. Counting of supporting reads beyond the threshold is
+ inaccurate, obviously.
+ Default: 300
+
+
+
+ Highly expressed genes are prone to produce artifacts during library preparation.
+ Genes with an expression above the given quantile are eligible for filtering by the 'in_vitro' filter.
+ Default: 0.998000
+
+
+
+ The breakpoints of false-positive predictions of intragenic events
+ are often both in exons. True predictions are more likely to have at
+ least one breakpoint in an intron, because introns are larger.
+ If the fraction of exonic sequence between two breakpoints is smaller than
+ the given fraction, the 'intragenic_exonic' filter discards the event.
+ Default: 0.330000
+
+
+
+
+ Only report viral integration sites of the top N most highly expressed viral contigs.
+ Default: 5
+
+
+
+ Ignore virally associated events if the virus is not fully expressed,
+ i.e., less than the given fraction of the viral contig is transcribed.
+ Default: 0.050000
+
+
+
+ Note: Increasing this value beyond the default can impair performance and lead to many false positives.
+ Default: 100
+
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+
+ Default: 0.070000
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+ Default: 10
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+ Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a
+ preceding program using the BAM_FDUP flag. This makes sense when unique molecular
+ identifiers (UMI) are used.
+
+
+
+ To reduce the runtime and file size, by default, the columns 'fusion_transcript',
+ 'peptide_sequence', and 'read_identifiers' are left empty in the file containing
+ discarded fusion candidates (see parameter -O). When this flag is set, this extra
+ information is reported in the discarded fusions file.
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+ If assembly of the fusion transcript sequence from the supporting reads is incomplete
+ (denoted as '...'), fill the gaps using the assembly sequence wherever possible.
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+ output_fusions_discarded == True
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+ output_fusions_vcf == True
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+ output_fusion_bams == True
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+ input_params['input_source'] == "use_fastq"
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+ visualization['do_viz'] == "yes"
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diff -r 000000000000 -r a24ca22b906e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,311 @@
+
+ 2.3.0
+ 0
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+ arriba
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+ 10.1101/gr.257246.119
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+ arriba -h | grep Version | sed 's/^.* //'
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+ By default the transcript isoform with the highest coverage is drawn.
+ Alternatively, the transcript isoform that is provided in the columns
+ transcript_id1 and transcript_id2 in the given fusions file can be drawn.
+ Selecting the isoform with the highest coverage usually produces nicer plots,
+ in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
+ However, the isoform with the highest coverage may not be the one that is involved in the fusion.
+ Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
+ For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
+ which reflect the actual isoforms involved in a fusion.
+\ As a third option, the transcripts that are annotated as canonical can be drawn.
+ Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
+
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+ The fusion of interest is drawn as a solid line in the circos plot.
+ To give an impression of the overall degree of rearrangement,
+ all other fusions are drawn as semi-transparent lines in the background.
+ This option determines which other fusions should be included in the circos plot.
+ Values specify the minimum confidence a fusion must have to be included.
+ It usually makes no sense to include low-confidence fusions in circos plots,
+ because they are abundant and unreliable, and would clutter up the circos plot.
+ Default: medium
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+ Exons usually make up only a small fraction of a gene.
+ They may be hard to see in the plot. i
+ Since introns are in most situations of no interest in the context of gene fusions,
+ this switch can be used to shrink the size of introns to a fixed, negligible size.
+ It makes sense to disable this feature, if breakpoints in introns are of importance.
+ Default: TRUE
+
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+ This option only applies to intergenic breakpoints.
+ If it is set to a value greater than 0, then the script draws the genes
+ which are no more than the given distance away from an intergenic breakpoint.
+ The keywords closestGene and closestProteinCodingGene instruct the script
+ to dynamically determine the distance to the next (protein-coding) gene for each breakpoint.
+ Alternatively, instead of specifying a single distance
+ that is applied upstream and downstream of both breakpoints alike,
+ more fine-grained control over the region to be shown is possible by specifying four comma-separated values.
+ The first two values determine the region to the left and to the right of breakpoint 1;
+ the third and fourth values determine the region to the left and to the right of breakpoint 2.
+ Note that this option is incompatible with squishIntrons.
+ Default: 0
+
+
+
+ ^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$
+
+
+ Occasionally, domains are annotated redundantly.
+ For example, tyrosine kinase domains are frequently annotated as
+ Protein tyrosine kinase and Protein kinase domain.
+ In order to simplify the visualization, such domains can be merged into one,
+ given that they overlap by the given fraction.
+ The description of the larger domain is used.
+ Default: 0.9
+
+
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+ By default the number of an exon is printed inside each exon,
+ which is taken from the attribute exon_number of the GTF annotation.
+ When a gene has many exons, the boxes may be too narrow to contain the labels,
+ resulting in unreadable exon labels. In these situations, i
+ it may be better to turn off exon labels.
+ Default: TRUE
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+ Whether light and shadow should be rendered to give objects a 3D effect.
+ Default: TRUE
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+ By default, the script colorizes domains according to the colors
+ specified in the file given in --annotation.
+ This way, coloring of domains is consistent across all proteins.
+ But since there are more distinct domains than colors,
+ this can lead to different domains having the same color.
+ If this option is set to TRUE, the colors are recomputed for each fusion separately.
+ This ensures that the colors have the maximum distance for each individual fusion,
+ but they are no longer consistent across different fusions.
+ Default: FALSE
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+ Default: Helvetica
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+ By default, transcripts are scaled automatically to fill the entire page.
+ This parameter enforces a fixed scale to be applied to all fusions,
+ which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable.
+ A common use case is the visualization of a gene that is found to be fused to multiple partners.
+ By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage
+ in a single plot one above the other with matching scales.
+ Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn,
+ or else dynamic scaling is applied, because display errors would occur otherwise.
+ The default value is 0, which means that no fixed scale should be used
+ and that the scale should be adapted dynamically for each fusion. Default: 0
+
+
+
+ When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes.
+ The plots can be cropped at a fixed level by passing a non-zero value to this parameter.
+ When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level.
+ When two comma-separated values are given, the cutoffs can be specified independently for the two plots.
+ A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage)
+ and that the coverage plots of both genes should be on the same scale. This is the default behavior.
+ A value of 0,0 also indicates that no cropping should be applied,
+ but the coverage plots of the two genes have different scales:
+ each one is scaled individually to the peak coverage of the respective gene.
+ Default: 0
+
+ ^\d+(,\d+)?$
+
+
+
+
+draw_fusions.R
+ --fusions='$fusions'
+ --alignments='Aligned.sortedByCoord.out.bam'
+ --annotation='$genome_gtf.annotation'
+ --output=fusions.pdf
+ #if $visualization.cytobands
+ --cytobands='$visualization.cytobands'
+ #end if
+ #if $protein_domains
+ --proteinDomains='$protein_domains'
+ #end if
+ ## Visualization Options
+ #if $visualization.options.transcriptSelection
+ --transcriptSelection=$visualization.options.transcriptSelection
+ #end if
+ #if $visualization.options.minConfidenceForCircosPlot
+ --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
+ #end if
+ #if $visualization.options.squishIntrons
+ --squishIntrons=$visualization.options.squishIntrons
+ #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
+ --showIntergenicVicinity='$visualization.options.showIntergenicVicinity'
+ #end if
+ #end if
+ #if $visualization.options.mergeDomainsOverlappingBy
+ --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
+ #end if
+ #if $visualization.options.sampleName
+ --sampleName='$visualization.options.sampleName'
+ #end if
+ #if $visualization.options.printExonLabels
+ --printExonLabels=$visualization.options.printExonLabels
+ #end if
+ #if $visualization.options.coverageRange
+ --coverageRange='$visualization.options.coverageRange'
+ #end if
+ #if $visualization.options.render3dEffect
+ --render3dEffect=$visualization.options.render3dEffect
+ #end if
+ #if $visualization.options.optimizeDomainColors
+ --optimizeDomainColors=$visualization.options.optimizeDomainColors
+ #end if
+ #if $visualization.options.color1
+ --color1='$visualization.options.color1'
+ #end if
+ #if $visualization.options.color2
+ --color2='$visualization.options.color2'
+ #end if
+ #if str($visualization.options.pdfWidth)
+ --pdfWidth=$visualization.options.pdfWidth
+ #end if
+ #if str($visualization.options.pdfHeight)
+ --pdfHeight=$visualization.options.pdfHeight
+ #end if
+ # fontFamily
+ #if $visualization.options.fontFamily
+ --fontFamily=$visualization.options.fontFamily
+ #end if
+ #if str($visualization.options.fontSize)
+ --fontSize=$visualization.options.fontSize
+ #end if
+
+
diff -r 000000000000 -r a24ca22b906e static/images/draw-fusions-example.png
Binary file static/images/draw-fusions-example.png has changed
diff -r 000000000000 -r a24ca22b906e test-data/Aligned.out.bam
Binary file test-data/Aligned.out.bam has changed
diff -r 000000000000 -r a24ca22b906e test-data/Aligned.out.bam.bai
Binary file test-data/Aligned.out.bam.bai has changed
diff -r 000000000000 -r a24ca22b906e test-data/Aligned.out.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Aligned.out.sam Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,89 @@
+@HD VN:1.4 SO:coordinate
+@SQ SN:22 LN:269079
+@SQ SN:9 LN:515509
+@PG ID:STAR PN:STAR VN:2.7.8a CL:STAR --runThreadN 12 --genomeDir tempstargenomedir --genomeLoad NoSharedMemory --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --limitBAMsortRAM 122880000000 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM ch --outSAMunmapped Within --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --outSAMattrIHstart 1 --winAnchorMultimapNmax 50 --chimSegmentMin 12 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --twopassMode Basic
+@CO user command line: STAR --runThreadN 12 --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outSAMunmapped Within --chimSegmentMin 12 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 122880000000 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1
+BCR-ABL1-46 163 22 225687 60 71M2994N7M1344N72M = 225737 5255 AACTGGAGGCAGTGCCCAACATCCCCCTGGTGCCCGATGAGGAGCTGGACGCTTTGAACATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTG CCCGGGGGG=GGGJJJGGJJJGGJJJJCJJGGJJGCJGCGGGC8J8JGGJJJJJGJJC(JGCCG=GGJJGCCCGC8GCCGGGGGG=GGCGGG1GG=GC1G=CJCJJCCCGGCGG1CGG1GGGGGGGG=GGGGGCCGCGGG8GGGCGG=GG NH:i:1 HI:i:1 AS:i:285 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-72 163 22 225696 60 62M2994N7M1344N81M = 228752 5264 CAGTGCCCAACATCCCCCTGGTGCCCGATGAGGAGCTGCACGCTTTGAAGATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCA CCCCGGGGGGGGGGJGJCCCJ1GJJJJGCGGGCJJJ=C1JJGGJGG8JGC=CCGJ1JGG8GGGGGJCGJCCGGGCG=CGGGGGGCGG=GGCGGG=8CCGCGGJJJ=JGGGCGGGGGCCGCCGGGGGGGGC=CCGCG8GGGGGC1GGGGCC NH:i:1 HI:i:1 AS:i:290 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-46 83 22 225737 60 21M2994N7M1344N105M717N17M = 225687 -5255 GCTTTGAAGATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGG =GGCGGGGGGG=GGGCCCGCCCGGGGGGGGGGCCGGGGCGG8CGCGGG1JGGCCGG(C=GCCCGGGGGGCGGGGGCGCGGCGGJCGGGJJGJGGGJJCGGGJJJGJJJJJJJGJJJJGGGJJJJJGGJJJJJGCJJJCGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:285 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-72 83 22 228752 60 3S7M1344N105M717N35M = 225696 -5264 TCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAAT =GGGGGG==GGGGCCCC=GGGGG=GGGGCGGGCGGGGGGG=CGGCCGCCJGGCGGGGG=GGG8GGGCGGC=G=CCJGGGGGGCGJJGJJCGGGGGGJJJGCJCCGJG=JJJGJGJJCJJJJGJJJJJJJ=GCJGJGCGGG=GGGGGGCC= NH:i:1 HI:i:1 AS:i:290 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-4 99 22 230111 60 97M717N53M = 230176 889 AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCC C==GGGGGGGGGGJJJJ1JJJGGJJGGJGGJJGJJCJGJGJJCGGCJGCJJJJCGJGGGGJGGGGGGCCGG8JGGCGCGG=GGGGGGGGGGGGGG=GCCGJGGGCCGGGGGG1GGGGGGCGCGGCGGGGGG=GGGGGGGGGCCGCGGGCC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 XS:A:+ NM:i:0
+BCR-ABL1-18 99 22 230118 60 90M717N60M = 230165 882 CCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGTAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCAATCAGCCACTGGAT CCCGGGCGGGCGGJGJJJJJJJJJ=GCJJCJJJJJGJJJGJJGJJJCGGJJGGJCGJC=GG8GCGJGCGCG==GGGCGGGGG1CCCGCGGGGGCGGCCGGC=GCGGG=GGGGCGGGGCGCGGGGGGG=GGGCGGGG(GGGCGGGCGCCGG NH:i:1 HI:i:1 AS:i:266 nM:i:2 XS:A:+ NM:i:2
+BCR-ABL1-12 163 22 230132 60 76M717N74M = 230923 868 GAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCA CCCGGGGGGGGGGJGGJJJJJCCJJCJJGJJGJJGGCJJJCJCGGGJJ=CGJGJJJJGGCGGGJJJ==GG(GGC=GGGGGGCGCGG(GGGGC1C8GCC=GG=C=CCJGGGGGG8CGGCCCGCGGGGGGGGCGGGG=GGGGGCGGGG=GGC NH:i:1 HI:i:1 AS:i:227 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-18 147 22 230165 60 43M717N75M32S = 230118 -882 CTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTT =GCGGGGG(GGGGGGGGGGGCC=GGC=GGCGGCCGGGGCGGG8JJJJ=GCGGGGG1GGGCCGGGCCGGGCGGCGGGJGC8GCCGCGGCG=GJCGJJGC8GC1JGG=GJJCJC1JGJGGJJJGJGCJJJ=1JJJJ=JGGCG=GGCGGGCCC NH:i:1 HI:i:1 AS:i:266 nM:i:2 XS:A:+ NM:i:0
+BCR-ABL1-4 147 22 230176 60 32M717N75M43S = 230111 -889 CCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGG CGGCGGGGGCGGCGCCG=GCGCGGGG8GCG881CGG=C=GCCGJJCJCCCGGG8GGCGG=GGGCCCGGCGGCCCCGGCGGGG=GGCGCJJGCGGJG1JGJJJ8JGJJCJJJ(JJGJGJJJGGJJGJCC1JJCGGJGG=GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 XS:A:+ NM:i:0 SA:Z:9,275100,-,107H43M,60,0;
+BCR-ABL1-12 83 22 230923 60 19S77M54S = 230132 -868 CGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAG 8CCCGGCCGGCCGGGGGCGG1CCG=GGCGGGGGC1GGGGCCGCGGGGCCJGG=CGGCGGGGCGCGCGGGCGGCGGJG==GGCGCJGCGGGCJGGGGGGGCJGJGGJJJGJGGGGCJJJGJJJGGJGJJJGJJCCJJGGG1GGGGGGG=CC NH:i:1 HI:i:1 AS:i:227 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-60 2145 22 230961 60 39M111H 9 275110 0 TCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA =CCGGCGGGGG=GJJGJGGGCJJCJJGJCGJG(J(JJJG NH:i:1 HI:i:1 AS:i:38 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,39S111M,60,0;
+BCR-ABL1-76 2145 22 230973 60 27M123H 9 275139 0 CAGCCACTGGATTTAAGCAGAGTTCAA CCCGGGGCGGGCGJJJJJGJJJGJJJJ NH:i:1 HI:i:1 AS:i:26 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,27S123M,60,0;
+BCR-ABL1-28 2209 22 230978 60 22M128H 9 275128 0 ACTGGATTTAAGCAGAGTTCAA CCCGCGGGGGGGGGJ=GJCGJJ NH:i:1 HI:i:1 AS:i:21 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,22S128M,60,1;
+BCR-ABL1-64 99 9 275097 60 6S144M = 275140 756 AGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGG CCCGGGGGCGGGGGJJJGJJJGGJJJJJCJJJJGGJJJGJJGJGJG=GGJG=JJJJCGCCC==JGGCGGGCJG1CCCCGG8CGGGGGGGGCCGC=CGCGGJGGGGCGCGGGGGGGGCCGCGGGG=GCGGGGGGG=GGGGCGGGGGGCCGG NH:i:1 HI:i:1 AS:i:290 nM:i:2 XS:A:+ NM:i:1
+BCR-ABL1-54 99 9 275097 60 61S89M = 275097 140 CCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTGAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTC CCCGGGGGGGGGGGJJJJJGJ=JJJJJJGJJJGGJJJJJJJCJJG8JJJGJJGJ=GG=JJJGGCGGCGGJGC(GGGGGCGC8CGGCGCCGGC=GGGCGGGJG1GGGGGG1CG=GGGGC=1G1CGGGGGCCGGGGCGG=CC=C=CGGGGG8 NH:i:1 HI:i:1 AS:i:219 nM:i:4 NM:i:2
+BCR-ABL1-54 147 9 275097 60 10S140M = 275097 -140 AAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACGTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTT =GGGGGGGCCCCGCCGGG=G(GGGG=CGCGGCGCCGG=GGGGGCJJJ=GC8C1GGGGGCG8GCCGC=GGG1GCCGGJC8GCGGCGCGJGJJJG1CGJGG=CJJJGGGGJG=CJGJJJJCJCJJGGJJJJJGGJGGJJCGGGGGGGGG=CC NH:i:1 HI:i:1 AS:i:219 nM:i:4 NM:i:2
+BCR-ABL1-48 163 9 275097 60 3S147M = 275137 753 GTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCA CCCGGGCGGGGGGGJ1JJJJJJJCJJJCGJJCGGJCJJGJGGJJJGGGCGJJ=GJJJG=JCG=GJGGGC8=GCG=G=GCCGGG1CG1GC=GGG8GGGGG1GCJJCJJCCGGCGCCG=CGCGGGCGG=GCGGG1CGC1CGC=CGGGCGGGG NH:i:1 HI:i:1 AS:i:295 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-2 99 9 275097 60 62S88M = 275097 134 TCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCCTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCT CCCGGGGGGGGGGGJ1JJJJJJ=JGGGGJJJCGCJJJCJJJJGGCJGGGJCJGGJJGJCGJGG1GCG=CGG(G=CGGG1GGCCGGGGGGGCGGGG=GCCGJGGCGCGGGGCCCG1GGGCCGGG8GGCGGCGG=CC(G=GC1GGCCGGGCG NH:i:1 HI:i:1 AS:i:214 nM:i:3 NM:i:2
+BCR-ABL1-2 147 9 275097 60 16S134M = 275097 -134 GGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTAT CGGGC=GGGGG=GGGGGGCCCCG=GG8=8CCGCGGGGGCGCGCJJCJ=CCCCC81GGGGC=GGGC8C8GGCGCGJCCGG8JCCGCC1GGCGGCJGGGJJJGGJJJJJCGGJGCJJJJJJG=JGJGJJJJGJJJGGJGCGCGGGGGGGCCC NH:i:1 HI:i:1 AS:i:214 nM:i:3 NM:i:1
+BCR-ABL1-76 99 9 275100 60 27S123M = 275139 752 CAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTG CCCGGGGCGGGCGJJJJJGJJJGJJJJJJJJJGJ1JCJJGJGGJJJGJJGGJJJ8GGJJGGGJJ=GGCGGGGGG=GGCCGGG8GC=GGGG=GCGGCGGGGJGG=GGGG=GGGGGGGGCGGGGCCGGGCG=GG(G=GCGCCG1CCGGCGGG NH:i:1 HI:i:1 AS:i:273 nM:i:0 ch:A:1 XS:A:+ NM:i:0 SA:Z:22,230973,+,27M123H,60,0;
+BCR-ABL1-68 99 9 275100 60 1S149M = 275125 175 AAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGA CC1=GC=GGGGGGJJJJGJJJJJGGJJJJJJJGJJJJJ=(GJGGG8CCGJJ=GJGGGGJGJGJ=GGGCCGCGGCG1CGCGGGGGGGCGCCGCGGCGGGGGJGCC8GCGGGGCGGC=GGGGG=GGGCCC=GCGGGGGGCGCGGGCGGCGCG NH:i:1 HI:i:1 AS:i:291 nM:i:3 NM:i:0
+BCR-ABL1-60 99 9 275100 60 39S111M = 275110 160 TCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCA =CCGGCGGGGG=GJJGJGGGCJJCJJGJCGJG(J(JJJGGCGGGJJJGCJGGG1G=JGGJJGCJCCGGJ(JJCCGCC=GCGGGCGGGGG1GGGGCGCGG(JCGCGGGGGGGGGGGGCCGGCGCGCGGGGGGGCGGGGCGG1GGGGGGCGC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 NM:i:0 SA:Z:22,230961,+,39M111H,60,0;
+BCR-ABL1-28 163 9 275100 60 22S128M = 275128 741 ACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCCCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTG CCCGCGGGGGGGGGJ=GJCGJJJ1JCJJJJGJJJJJCCJJJJG8JJCC=CGGCGGJGGC(JGGG=GCCGCGCJ8CGGG=GGGCGGGGGCGGCCGGCCGGGCCJ=JC=CGCGCGC1G8GCCGGGGGC=GCGGGCGGGGGGGGGGGGGCGCC NH:i:1 HI:i:1 AS:i:274 nM:i:2 ch:A:1 XS:A:+ NM:i:1 SA:Z:22,230978,+,22M128H,60,0;
+BCR-ABL1-4 2193 9 275100 60 107H43M 22 230111 0 AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGG CJJJ(JJGJGJJJGGJJGJCC1JJCGGJGG=GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:42 nM:i:0 ch:A:1 NM:i:0 SA:Z:22,230176,-,32M717N75M43S,60,0;
+BCR-ABL1-60 147 9 275110 60 150M = 275100 -160 GCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCT GCGGCCCGCGG=GG8GGCGGGGCCGCC=GCGCGGCG1GGCGG1JCJJ8CCCG=GGGGGGCG=GCGGGG18CCGCG=GGGG1CGG8C=GGGGCGGCJGJGJGJGJJGGJGJJJGJGJJJGGJC(JJJGJJJGJCJJGCGGGGGCGGGGCC= NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 NM:i:0
+BCR-ABL1-68 147 9 275125 60 150M = 275100 -175 TGACTTTGAGCCTCAGGGTCTAAGTGAAGCCGCTCGTAGGAACTCCAAGGAAAACCTTCTCGGTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGG G=CGGCGGGCCGCGCGGCCGG8GCCGCC(GGC=8=GGG=GGGCJ1=JJCCGGGCGGGGGGGG=GCGGGGCGCG==GGCGGGGGJGCCJJGGCCG=GCCCGGJCGGJJJJJ=GJJJJGJCJ=GCJGJGJJJC1GGJJJGGG=GG1GGGCCC NH:i:1 HI:i:1 AS:i:291 nM:i:3 NM:i:3
+BCR-ABL1-50 99 9 275125 60 150M = 275169 757 TGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGG CC1GGCGCGGGG=JGCJJJJJGJJJGJJGGJJGJJ8JGCGJJJJJJ8CJJGJJCGJGGGGJJCCG=CGGGGGCCCG=CGGCCGCGGGGGCGG=GGGGGGGCCGGG==GGGGGCCGG=GGGGCCG=GGGGGCCC=GGCGGGGCCGGCCGGG NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-28 83 9 275128 60 146M563N4M = 275100 -741 CTTTGAGCCTCAAGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGA GGGGGCGGGG=C1=8GGCGCGGGCGCGGGGG=GC=GGGGCG1CCCGCGGCCGGGC=GG=GGGGGCCGGGGCGGGCGJJGGGGCGGJ1JGGGGCGGJGJGGJJJCGGCJJCGJ=GJGCGGJJJJGGJJG1JJJGG1JJ=GGCGCGGG1CCC NH:i:1 HI:i:1 AS:i:274 nM:i:2 ch:A:1 XS:A:+ NM:i:1
+BCR-ABL1-48 83 9 275137 60 137M563N13M = 275097 -753 TCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCG GGGCGGCGCGGGG8GGGGGCGGCGGGCG1GCGCGG8GCGGCGC1G8CCGCGCGGCCGGGGGCGCCGCC1=CCCCGCCJCGGGGGGJJGJC=CCJ8JJC=JJCGCJJJGJJJJJJJJJJGJJGGGCJJJJJJJGJGJGCGGCGGGCGC=C1 NH:i:1 HI:i:1 AS:i:295 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-76 147 9 275139 60 135M563N15M = 275100 -752 AGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGG CGGCGGGGCGGGGGGCGCCGCGCGGGGC=GGCGCCGCGCGGGCJJCJC1GGGGG=GCGGGGG=GGGGGGGGGGGGGCGGCGGGGGGJGJCGJGGJGJCJGJJJJJG8JJCJGG1JJJJJJJG8(JJJJJGJJJGJJJGGGGGGGG1GCCC NH:i:1 HI:i:1 AS:i:273 nM:i:0 ch:A:1 XS:A:+ NM:i:0
+BCR-ABL1-64 147 9 275140 60 134M563N16M = 275097 -756 GGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTGTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGT C=GGGGGCGGCGGGGGGC=GGGGC1CG=1=GGGCCC=GGGCGCCCCJJGCGCGGGGCGGCGCGCCGCCGCGGGGGCGC1GGGGG=GG1CGJGJJJ(CCGGJJGCGJGJGJJJGGGCGJGJJJJJJJJJGJGJGJJJCGCGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:290 nM:i:2 XS:A:+ NM:i:1
+BCR-ABL1-14 99 9 275146 60 128M563N22M = 275170 737 GAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGG CC=GGGGGGGGGGJGJJCJGJJJGG1JJGJ=JGGGJJJJGGJJJGCJJCGJJGC=GCJGGJGGCGGGCCGGGCGGCGCGGGGGGGGGGGGCC8GGGGCGCJCGGGCCCGCG8GGGGCGGGCGGCGGGGGGCGGGGGCGGG=GGGGGGCCG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-78 99 9 275151 60 123M563N27M = 275200 762 AAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATA CC=1G=GGGGCGGJJJJGJJGG8JJCJGJGJJ8JJJJGJCGJGJJ=JGGGCGJCJCGGG=JJJJGGG=JGC=GGGCGGGGGGCGGCG=GCCGGGGGGCGGJCGCCGCGGGGGGGCCGGGGCGCCGGG=GGGCGCGGGGCGGGCCGGGGGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-62 163 9 275157 60 117M563N33M = 275215 771 CTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACA CCCCGGGGGGGGCJGGGJJGJJJJJJJ=GJJCJJGJCJGJCGCGCGGGCCJGJCGJ81JC1GGGGGCG8GGCGGGGCG1C1GGGGCGGCGCCCGGG=GC=CGCJJJJGGGGGCGGCGC=8GCCGGGGGGGG=GCG=1GGGCGGGCGG1CG NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-50 147 9 275169 60 105M563N45M = 275125 -757 CCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGT CCGCCCGGGGGCGGGG1GCGGGGGGC8CGG=CGGCCC=CGGGCCJ(JJ=GGCGCGGGGCGGGGGCC8GCCCGGCGCGGGJ8GGGGCC1JJGJCGGJJJGJG8JJGJJJJCJJJGGJGGGCJGGJJJJGGGJJJ=CJCGG=GCGGGGG=CC NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-14 147 9 275170 60 104M563N46M = 275146 -737 CAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTG 1CGGGGGCGGCCGG1CG=GGGGGGGCGGGGGCCGGG1CGCGCCJJJJJCG1CGGGCCGCGGGGGGGGGGGGCGGGGGGGCCGGGCGJJGG=JJ(J18GJCJGJ8JJGGJ=JJGJJGGGJJJ=JJJJCJJJJJJJJJGGGGGGG1GGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-20 163 9 275172 60 102M563N48M = 275219 760 AGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTG CC=GGGGGGGGGGJJGJJJJJJCJJ=JJJJGGGGJCJJGCGCGJGGCCCJJJGJJJJCGGJG=GGJGGGGGJGJGCCGGGGCCG=GG=C=G=GGCCGGGCGCCCC=JG11GGCCGCCCGCGCC8CGGGGCC1CGCGGG=GG=CCC1GGCG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-26 163 9 275174 60 100M563N50M = 275216 755 GAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGCAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAA C1CGGGCGGGGGGJJJ=JJGGCGGGJJGJJGGJGGJJGJCJGJJ=GGCJJGJJGGCGCGCGGG=JGGG8GGGGCGGGGGCGCCCGGGCGGGCCCCCG=GGGCJ(JCJ=GGCCGGGGGGGGGGGGGCCGCGGGCCGGGGGCGCGGGGGGGG NH:i:1 HI:i:1 AS:i:298 nM:i:2 XS:A:+ NM:i:1
+BCR-ABL1-34 99 9 275183 60 91M563N59M = 275223 753 CTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCCCTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACC CCCGGGGGGGGGGJJJJJGJGJJGG=JJJJJJGJJJGJGJC1JGGGJGGJJGGGJJGG=GCGJGGJCGGGGGGCG=GGCGG1CGGGG=CGGCCGGGCGGGJ88=CGCG=GGGGGC=GGCGGGGG1GGCCGGGG1GGGCGGGGCCCGCGGC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-80 99 9 275199 60 75M563N75M = 275250 764 AAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAACTGGCCAAGGCT CC=GGGGGGGGGGJJJJCJCJJJJJJGGGJJJCJGCCJJJJJ=JCGJJJ=J8JGJGJ=J=JGG=CJCCGG1GG=CGGG=8GG=GCGCCGGCGCGGGG8GGJG1CGCGCCGCCGCGG=GGGGCGCGGGGGG=G==GGCC(GGCGGGGCGCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-8 163 9 275199 60 75M563N75M = 275246 760 AAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCT =C=GG(1GGGGGGJGGJGCCJJCJJJJJJ=GJGGJJGJ=JJGCGCGJJJJJGGJ1GGJJG8C8GGG=GCCG8GGGG1=CGG88CG=GG8GG=GGGCGG8GGCJ18CJ=CGGCGGGG1CC=GCCGCGGG=GGGCGGCGCC8GCCGCGCCGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-78 147 9 275200 60 74M563N76M = 275151 -762 AAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTG GGGGGCG8GGGGGGGCCGCGG=GCCGCGCGCGGGGGGGC=GCGJ88JJ=CGCGGGG=CGGGGG(GG=G(CCGCGGCJGJGGGCCGGCCJJGGJJJGJJGG1G(JJJGCGJJG=J=GJJJGJJJJJ=CGJJJGJGGJJGGCGGCGGGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-42 163 9 275204 60 70M563N80M = 275245 754 GACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTC CC=GGGGGGGGGGGGJJJGGJJJ=JJJGGGJJGJGCJJJJ(GJGJJCCJGGGJCGJGGJJJGG=G1C8GCGGGG18GCC=GGGGGCCCGC1GGGGCGGCGG=CCJCCGGG==GGGGGGGG1G(GGG=C=GGGG88=CC=GGCGGGGCGGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-62 83 9 275215 60 59M563N91M = 275157 -771 TTTCGTTGCACTGTATGATTTTGTGGCCGGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTA GCCC1CCCCCGCGCCC=GGGGGGCCGGC8CGGC1GGC=CGGGGCCCGGC8GCC=GCGGGCGGGGGGGCCGJGGGGGGGGGJGG=GJGCGJGGJ=JJGJGJCG=JJJJGJJJJGJJJGJJGCGJCJ=JJJJJGJGGJJGGGGCGGGGGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-26 83 9 275216 60 58M563N92M = 275174 -755 TTCGTTGTACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTAC CGGGGGC(GGGCGGCGCCGGGCGGCGCCGGGCGCGGGGCGGC==GGCCG=1GCCGGCGGCGGGCCCGGG=GGGCGCCCCJJGCCC1GJJCJGGGJJJG8JGG=GJJ=GGJJJJCJGCCGJJJJJJGJJJJJGGJGJJGGGGGGGCGCCCC NH:i:1 HI:i:1 AS:i:298 nM:i:2 XS:A:+ NM:i:1
+BCR-ABL1-44 163 9 275217 60 57M563N93M = 275260 756 TCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACA C=CGGGGGGCGGGJJJJJGJGJJJJJ1JJJJJJ1JJJGCGGG=JGJGJGGJGGCGGCGJGCJG=JJGGCJCGCCCGGGGCCCGGGC=GG=CGGGGGGGGGGGCJJJJGC=GGGGCGGCGGC=CCGG8GGGCGCGGCCCGGCG=GGCGGGC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-40 99 9 275219 60 55M563N94M1S = 275838 769 GTTGCACTGTATGATTTTGTGGCCCGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATG CCCCGGGGGGCGGJJJJGGJCJJJ(GJJ=JJJJJCJJJGGGGJJJGGGJJCJJJGJCJCCJJ(CJ=CGGGJ=GGGCJCGGGGCGGGCGGGGGCGGCGGGGCCGGCGCCGGGGGGCCGCGGGGGGGG=GGGCGG=GGGGGCGGG8G=CGG1 NH:i:1 HI:i:1 AS:i:297 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-20 83 9 275219 60 55M563N95M = 275172 -760 GTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATC GCG=GGGCC8GCCGCGGGGGGG=GGCCGGCGGGGCCGGGCGG8CGGCGGJGCGGCGGGGGGCGG=GGG1GCGGGGGGGGGC==JJGG=GGGCCJGGGGGGJJJJJGCCGJJGGJGJCJJCJJJJJGGJJJJGJJJJ1GGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-34 147 9 275223 60 51M563N99M = 275183 -753 CACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGC CGGG8GCC=GGGCGGGGGGCGGGGG=GGGGGGGCGGCGCGGGGJJJJCCCGC1GGGGG8GGCC=GGGGGGGGGGGCCGGCCCG=GCJJJGGGGGG81J8=CGJGGGGJGJJCJGGJGGJGCCJJGJJJJJCJJJJGJGGGCGGGG=GCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-22 99 9 275237 60 37M563N113M = 275864 777 GTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTG CC1GGGGGCGGGGGGCJJGCGJCJJJJJJJJGJJJJGJJGGG1JGCJJCJJGJJJJJGGGGJGJJCGJJGCC8CGGCGCGGCGCCG1GGCCCCGC=GG=GJCGGGGCGCG=GGGGGCGGC=CGGGGGGGGGCGGCCCGGG(G8GGGGGGG NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-42 83 9 275245 60 29M563N121M = 275204 -754 TGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACA GGGCGGGCGCCGGGGGCGGGGGG=CGGGGC1CGCGGGCG=GGCG=GGCCCGGGGCGCGGCGGCCGGGGGGG(GG=GGG=GGGCCGGJJGJJ=GGGGGJJGCGJGGJJJJJJGCJGJGG(GGJJJGJJJJJJJ8GJJJCGGGGCGG1G1CC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-8 83 9 275246 60 28M563N122M = 275199 -760 GGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACAC G=GGCGGGGG=GGGGGGGCCGCCGCGCGGCCGGCGGGCCGGCGGCGGGGJGG=GGGGGGGC=GCGGGCCCG=JGCG=GGGJGGGJGJGGGJCGCGCGGJGGJJJJJJGJGJGJJJG1JJJJJJJJGJCGGJJJJJJCGGGGGGGGCGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-80 147 9 275250 60 24M563N126M = 275199 -764 ATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCT CCCCCGGCC8GCG=CGCGCGGG(GGGGGGGGC=GGG=GG=CGCJJJJJGGGGC==G8CGGG=GCGGC1GGGC(GG=G=GGCGJC8GCGJGJCGCJGJGCGJGJJJGGJJGJGJCJJJJGJGJJJGGJJJJJJGJJJJ8GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-30 163 9 275254 60 20M563N130M = 275867 763 CACTCTAAGCATAACTAAAGGTGAAAAGCACCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTA CCCGG1GGGGGGGJGJCJGJGJJJ(JGJJ(JGJGC=GJJJGJJGGJGGJJJJGGJGGCCCCJG8CG=GCJCGGGJ=GCGJ1CGGGGCCGCG8CG=GGCGGC(CJJC=CGGCGG(CGGGGGGCGCCGG=GC1GCGG=G1CGGCCCCG===8 NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-52 99 9 275256 60 18M563N132M = 275877 771 CTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCCTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACC CCCGGGGGGGGGGGJJGCGJGG8GJJJGJJGJG=G=JJGGCJGGGGGJGGJJGJJGJGGGCJ=GJGGGCGJCGGGGGGG8CGGGGGGC=GGCGGGGCGCGJCGCGCCCCGCG11GGGGGGGGGGGGGGCCCGGGGCCGGCGGGGGCGGCG NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:1
+BCR-ABL1-44 83 9 275260 60 14M563N136M = 275217 -756 AAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGG CGGGCGCGGGGCGCGGGGGCGGGGGGGGGCGGGGGGGG=G1GGGCGCGGCGCGGGGGGGCGGCGCCGCGGC==GGG=1GGG=CJJGCGJGJJJCGCJJ8GJJGGGJJGGJJJGJJGJJJGJJJJJJCJGJ=GGJJ=JGGGGGCGGCGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-40 147 9 275838 60 150M = 275219 -769 TGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAA =GCCGGGGCGGGG=GG1G8G=G(GGCGGGGGGGGC1C=GCGG=J8JJ1GGGGGGGGGGGGGGGGGC=1G8CGGCJ8GC1GGCGCCGJG1GGJGGJGJ8JJCJJJGJ8GGJJJ=JGJJG=CGG=JJJJJJJ8JJ=JJGGGGGGGGGCGC=C NH:i:1 HI:i:1 AS:i:297 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-16 163 9 275840 60 150M = 275888 198 AAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCACCAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATG CC8GGG1CCGGGCCJJGJG(JJJJJ(JGJCJGJJJJJJJJGGJGJGJJCCJJJGJGGGGCGGG=C=JGJJG=C8GGGCGGGGGC(GGCGCGCGGCG(CGG=1(C=JCGGGCCGGGGGCGCGGGCGGCGGGCGGCCGGGGGGGG8GGGCGC NH:i:1 HI:i:1 AS:i:296 nM:i:1 NM:i:1
+BCR-ABL1-6 99 9 275846 60 150M = 275903 207 TCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTG CCCGGGGGGCGGGGJJGJGJ=JJJJJJJJJJGJGGJJJGGJC=GGGGJ=GGCJJJGCGJGJGJJGJGCGJGGJGJCGCGGGGGGGGGG8GC8GC8G=GGGJ=GCGGGGGCCGCCGGGGGGGG1G1=GCGC81CGGGGGCCCGGGGGCGGG NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-32 99 9 275850 60 150M = 275894 194 GGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTA CCCGGGGGGGGGGJJGGJJJ=JJGJ8JGJ=JGJG=GGGJGCCJJJC=J8JJ=GCCJC8JC=GGGJGG(GGCJGGGG1GC=GJ=GCCGGCCGGG=GGGGGGJGCGGCGG=CGGCGCG=GGC=CGGGGCCGGGGGGCCCCGCCGGGCCGGGG NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-38 163 9 275854 60 150M = 275900 196 TTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTG CCCGCGGGGGGGG=GGJGJGJJJ1=GGCJJJCGJ=GJJJGGCJGGCGJGGJJCGJCGJGGG=GGGGJCGGGGGGJGGGGGGGGG8C=G=GCGG==CG8GCG=JCJJCCGG8CGGCGGCCGGGCCGCGGCGGG=GCGGCGG=8CGGCGCG= NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-22 147 9 275864 60 150M = 275237 -777 ATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCG GGG1C8GGG=C=GGGCGCGG=GG=GCGGGGCGGGCGCGGGCGGJ1CCJCCC8GCC=GGCGGGGGGGCGCGCGGGCCGJGCGJGJGGJGCJGGGGGCGGGJ(JCGGGJJJJJJG=1GGJJJGJJJGGJJJJJJGJ1JJGG=GGGGGCGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0
+BCR-ABL1-30 83 9 275867 60 150M = 275254 -763 ACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGA CG8GC==GCGCCGGGGGGG8=CGGGGGC=CGGCGGGGGCG=GGGC=GCCJGGGGCGGCGCGGGGCGCGGGCCCGJGGG8(8GC8GCGCGCJGGGGGGJGGGJGJJJJJGJJJJCGGJJGJJJ=JJJJGGJ=JJJJGGGGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-36 99 9 275872 60 150M = 275919 197 GGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAAT CCCGGGGGGGGGGJJJGGJJ=JJJJGJJJJJ=GGJJJCJ=JGGGJGGJGJJGGGGCGCG=JGCCGJGCJGCGGGJGGCGCG1GJGC=8GGCCCCGG8CCGJCCGGGCGGGCGGGGGCG1GCCGGCGGGGGCCCGGCCCG(G8GC8=CCGC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-70 163 9 275874 60 150M = 275911 187 GGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGG CCCGGG==GGGGGJJJJJJJJJJJ=GJ8J=GJGJGJGGJCCJJJCGG1=GJGJG18JG=GGGC1GGGJ8GCCC1=CCGCGGG(GC1GCG1GCCGC8GG1GG=JJCJ1GGCGCCGCG(CGGCGGGGGG(GGGGGGCGCCGGGGCGCGCCG= NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-52 147 9 275877 60 150M = 275256 -771 ATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAG CG=GGGGC(CGGGGGGGCCGCGCCGGGGG=GGCC8CGGCCCCCCJ=CJ=GGGGGGGGCG=GGGGCG(GC1GGGC=GJCCCGJ=88GJGGJGJGCJGGJJGGJJJGJJJJGCGJJGGJ(GJGGJCJJJCJJJJJ=(JJGGGGGGGGGCCCC NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:0
+BCR-ABL1-56 99 9 275885 60 150M = 275928 193 AAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGG =CCGC=GGGGGG1JJJGJGJJJCJJCGJJJJJJJJJJCGJJJJJJGGCCJ1JGCGGCGJ8GG(CJGJGJCGGCGG1CC=CG=GCC=GGGGG=GGCGCCG1CGGGGGGG1GGGGGCGGGCGCGGCGG811G8CCGGGGCGGGGGCCG=CGC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-16 83 9 275888 60 150M = 275840 -198 CCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGC CGGGGGG=GGCGGGCGGGGGGGCGGGGCGGGGCCCG=CGGGGGCGGGCCCGG8GCCCGG8GCGGC=GCCCGGGGGGCGGGCGGJGGGCCGGJCGGJJGJGGGGGJJJJGJJGGJJGG=JGGJJGGJ=JGJJJJJJGJC1GGGG=GGG1C1 NH:i:1 HI:i:1 AS:i:296 nM:i:1 NM:i:0
+BCR-ABL1-32 147 9 275894 60 150M = 275850 -194 CCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGA 8GCCCCGGCGCGC1GGGGCGGCCGGGGCG1(GG=GG=GCGGCGJCJJCGG8=GGGCCGCGGGCGGGGGC=GC1=GGGGGJGGCCGJJCGGGJJJCGGG8CCGGGCJGJGJJGCCGCJJJJJJJJJJGCGJJJGJJGJGGGGGCGGGG=CC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-38 83 9 275900 60 150M = 275854 -196 ATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGA GCGCCGCGGGCGGGGGGGCGGCGCG8CGCGGGG8GGCGGGCCCCG8CC=JGCGGGGGGCGGGGCGCCGC=GCCCGGJGGGCGGGCJGCCJJGJG=GGCJJJGGJCGJCGCGJJJC=JJGJCJGJGJJGJJJ=JJJ1GGGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-6 147 9 275903 60 150M = 275846 -207 GCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCA CG8GCGGGCCCCGGCGCGGGGCCGGGCGG8CG=G=GCCGCGG=1CJ8JCCGCGGGGGCGGGGGGCGG=G=8GCGJG=GGGGGGJGCCGGJJGG=G=CJ8=JJJJGG=JJJJJGJJGJGJJGJJJJJCCCJJJGGJJJG1GGG1GGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-70 83 9 275911 60 150M = 275874 -187 TGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGC CGGGCGGGCGGGCCGGGG=GGG8GCGGG8GGCGGGCGGCGGGCGGGGG=JGGGGGCGCGGGGGCGGGGCGCG1GGGGCJC8GG=JGGJJCCCJJGGGGJGJGJGGJJGGJJJJJGCJJJJGGJJGJJGJJJGGGJJJGGGGCGGGGG=CC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-36 147 9 275919 60 150M = 275872 -197 AAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTC C=GGGGGGCCGGGGGGGGG=GGCCGCGGGC1GCGC1GCGGCCGJJ(CCG8GCCGGGCCGGGC=CC1CG=CGCCGGG=CGGGGGGGGCGGGGGJ==JJJJJ1CJJJGJGGJCGCJGJGJGJJJJ=GG1CJJCGJG1GC=GGGCGCGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-56 147 9 275928 60 150M = 275885 -193 CATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTCCATCTCGCT CCGGGCGCGCGGGCG=CCCGGCGCGGGGC=CGGCGGCCGCGGGJJJJCCGCCG(GCCCCCGGCCGGG=G8GGGGGGCC=C=CGGJGJJJGC=JGGJJJGJGJ1JJJGC=JJJG=JCJJJJJJJ=JJGGGJJJCGJJJGGGGGCGG=GCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0
+BCR-ABL1-74 77 * 0 0 * * 0 0 TCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTC CC11GGGGGGGGGGCCJJJGCGJJGJJJJJGGGGGGJJJGGJG==GCJCJ=GGJJGGJJGGCJGG=GGGGGJGGJGC=GC=GGGCGGGCGGGGCCGCGGGJCGC=GGC8CGCGCGGGGGGCGCC1GGCGCC=GCCGCGGC8GCGGGCCCG NH:i:0 HI:i:0 AS:i:155 nM:i:2 uT:A:1
+BCR-ABL1-74 141 * 0 0 * * 0 0 CATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAGGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG CCCGGGGGGCGCGJGGJJGGJGJJJGJGGJJGGJGJJ1=JCJJGGGJJJJGGGJGCCJGGJGG=J1JG8JGCGGGJG=GC1CGCCGGCG(GGCGGCGGGGGCJC1CCGC==CCGGGGCGGCGGGCCGGCGCGC8CCCCGGG=GGGC=GGG NH:i:0 HI:i:0 AS:i:155 nM:i:2 uT:A:1
+BCR-ABL1-66 77 * 0 0 * * 0 0 TCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAAACCCATAGAG CCC=GGGGCGGGGJJJJJGJJJJ=JJJGJJ1GJJGJJJJJGJJJJJGGGGCGJJGGGJJJGGCGGGGJGCGG1JCGGG=GCCGCG=GC=G=GCCGGGGG8JGGGGGGGGGGGG=GGCGGC8GGCCGGGC=GGGGGGGGG=CGG=8GGCCG NH:i:0 HI:i:0 AS:i:159 nM:i:0 uT:A:1
+BCR-ABL1-66 141 * 0 0 * * 0 0 CATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG CCCGGGGGGGGGGGGJ=JGJJJJJJJGGJJCCCJGJJ1JJJGCJGGGGJJJJ=GGGJGJGC(GGGGJGGGJG1=GGGGGGGG=G=C=GG8CC8GGGGGCCCCJCCCJGCG=GGCCGGCGGCGGCG==1GCCGGC1GGGGGCGGGGGGCGG NH:i:0 HI:i:0 AS:i:159 nM:i:0 uT:A:1
+BCR-ABL1-58 77 * 0 0 * * 0 0 ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGG CCCGGCGGGGGGGGJJJJJGJJGJGJGJGJJJJJJJJJCJGJJJJGCG=8GGGJGJGGCGGJGCGJJJCJGGG=CGCCGGCCGGGCGCGGGCGCG1GGGCCCGGGGCG8GCCC=C8CGCGG=CCCGCCCCGGG=CCGGCGGGCGGGGGCG NH:i:0 HI:i:0 AS:i:185 nM:i:3 uT:A:1
+BCR-ABL1-58 141 * 0 0 * * 0 0 TTGGGGTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATTCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATG CCCGGGGGGGGGGJJJJJJGJGJJJGGJ=JJJJJJJJGC=GJJGGJJGJJGG1GCJGGGG=JGGG8C=GCCGC==GGGCGGGGGG=GGG=(G=CCGCCGGGGCJJJJGGGC8GCGCGCG8CGGCCGGGCGCGCGG8CCGG8CGGGGGGGG NH:i:0 HI:i:0 AS:i:185 nM:i:3 uT:A:1
+BCR-ABL1-24 77 * 0 0 * * 0 0 CGCAGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGGCTGAGTGAAG CC11GCGGGGGGGJCGJGJJCCJJJJGJJJJGJJGGJJJCJJJG8JJJ1GJ=JGGGGJJJCG=8GGCGCCGGGCCGGGCGGGGCGGGGCCGCGGCCGGG=J1GCCC1(CCGGCGGGCCGCGGGCGGGGC=GGCGCCGCC1GCGGGGGCGG NH:i:0 HI:i:0 AS:i:154 nM:i:3 uT:A:1
+BCR-ABL1-24 141 * 0 0 * * 0 0 TTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAA C=CCGGGGGGGGCJ1GGJJJJ1JJJJJGJJ=GJJG8GGJ=GJGJJGJJGGGCGJGCGGGCGGG8GG=GJJGCG1GCGGJGCCGGCGGGCCGGGCG8GGGGG8C1==CGGCCCGCGGGGC8GCGGG8GGGCGCCGCCGCGGGCGGGGGGCG NH:i:0 HI:i:0 AS:i:154 nM:i:3 uT:A:1
+BCR-ABL1-10 77 * 0 0 * * 0 0 AGGTTGGGGTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACG CC=GGGGGGGGGG1GJJJJJCJJJJJJJJJJJGJ=GJJJGCJJJJCJGJGCJGJJJGGJJJGGCCGGJGC=GGJ1C8GGGGGGCGCCGGGGGGCGGGCGCCCG1GGCGCGCGGGCC8GCGCGCGC8CCCGCGCGGGGGCGGGGGCGGCGG NH:i:0 HI:i:0 AS:i:181 nM:i:2 uT:A:1
+BCR-ABL1-10 141 * 0 0 * * 0 0 ATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGA 1CCGGCGGGGGG1GGJJJGCC1JJJJCCG=JGGJJGJJJ=GGGGGJJGGGGGGC1J=CJGCGGGGCGC(CGGGGG=GGGGG(G=CGGCGGGGCCCGC=CCCCJJCC8G1GGGGCGGGGGGCGCGGGGGGGCG=GGCCGCCGCC1G=GGGG NH:i:0 HI:i:0 AS:i:181 nM:i:2 uT:A:1
diff -r 000000000000 -r a24ca22b906e test-data/cytobands.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cytobands.tsv Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,5 @@
+contig start end name giemsa
+22 1 40586 q11.22 gpos25
+22 40586 269079 q11.23 gneg
+9 1 21036 q34.11 gneg
+9 21036 515509 q34.12 gpos25
diff -r 000000000000 -r a24ca22b906e test-data/fusions.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fusions.tsv Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,2 @@
+#gene1 gene2 strand1(gene/fusion) strand2(gene/fusion) breakpoint1 breakpoint2 site1 site2 type split_reads1 split_reads2 discordant_mates coverage1 coverage2 confidence reading_frame tags retained_protein_domains closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1 gene_id2 transcript_id1 transcript_id2 direction1 direction2 filters fusion_transcript peptide_sequence read_identifiers
+BCR ABL1 +/+ +/+ 22:230999 9:275100 CDS/splice-site CDS/splice-site translocation 1 3 0 3 8 low in-frame . Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%) . . ENSG00000186716 ENSG00000097007 ENST00000305877 ENST00000372348 downstream upstream . AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR BCR-ABL1-4,BCR-ABL1-28,BCR-ABL1-60,BCR-ABL1-76
diff -r 000000000000 -r a24ca22b906e test-data/genome.fasta.gz
Binary file test-data/genome.fasta.gz has changed
diff -r 000000000000 -r a24ca22b906e test-data/genome.gtf.gz
Binary file test-data/genome.gtf.gz has changed
diff -r 000000000000 -r a24ca22b906e test-data/protein_domains.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/protein_domains.gff3 Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,83 @@
+9 pfam protein_domain 33502 33541 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 33992 34063 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 35324 35381 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 37391 37409 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 37479 37553 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 38833 38931 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 41390 41413 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 41489 41494 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 43744 43846 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 44647 44729 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 47496 47541 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 51664 51812 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013
+9 pfam protein_domain 102331 102396 0 + . Name=Zinc finger%2C C2H2 type;color=#80FF00;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF00096
+9 pfam protein_domain 102412 102480 0 + . Name=C2H2-type zinc finger;color=#80FF80;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF13894
+9 pfam protein_domain 114903 114949 0 + . Name=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382
+9 pfam protein_domain 116528 116596 0 + . Name=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382
+9 pfam protein_domain 121951 121971 0 + . Name=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985
+9 pfam protein_domain 123179 123300 0 + . Name=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985
+9 pfam protein_domain 275219 275273 0 + . Name=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018
+9 pfam protein_domain 275837 275922 0 + . Name=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018
+9 pfam protein_domain 275962 276132 0 + . Name=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017
+9 pfam protein_domain 283799 283855 0 + . Name=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017
+9 pfam protein_domain 283973 284071 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069
+9 pfam protein_domain 293165 293249 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069
+9 pfam protein_domain 293896 294073 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069
+9 pfam protein_domain 295904 296088 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069
+9 pfam protein_domain 299451 299603 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069
+9 pfam protein_domain 301104 301156 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069
+9 pfam protein_domain 306405 306716 0 + . Name=F-actin binding;color=#800000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF08919
+9 pfam protein_domain 314470 314862 0 - . Name=Orexigenic neuropeptide Qrfp/P518 ;color=#808000;gene_id=ENSG00000188710;gene_name=QRFP;protein_domain_id=PF11109
+9 pfam protein_domain 325106 325108 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147
+9 pfam protein_domain 325118 325359 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147
+9 pfam protein_domain 326270 326449 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147
+9 pfam protein_domain 332828 332924 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147
+9 pfam protein_domain 344780 344908 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147
+9 pfam protein_domain 430353 430623 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055
+9 pfam protein_domain 447321 447625 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055
+9 pfam protein_domain 453081 453209 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055
+9 pfam protein_domain 457203 457334 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 459902 460054 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 460070 460088 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 460167 460282 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 462677 462771 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 466560 466608 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 470157 470166 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052
+9 pfam protein_domain 473527 473719 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052
+9 pfam protein_domain 473886 474001 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052
+9 pfam protein_domain 477965 478038 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052
+9 pfam protein_domain 478042 478107 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 478144 478183 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 482071 482168 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 482175 482259 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 487996 488060 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 488076 488222 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 489116 489262 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 489945 490067 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+9 pfam protein_domain 490710 490856 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053
+22 pfam protein_domain 2420 2524 0 - . Name=Armadillo/beta-catenin-like repeat;color=#000080;gene_id=ENSG00000100218;gene_name=RSPH14;protein_domain_id=PF00514
+22 pfam protein_domain 36321 37004 0 + . Name=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503
+22 pfam protein_domain 63673 63981 0 + . Name=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503
+22 pfam protein_domain 90736 90740 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 93060 93112 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 93619 93720 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 96554 96622 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 98578 98629 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 99484 99565 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 99749 99839 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 101465 101502 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071
+22 pfam protein_domain 121553 121771 0 + . Name=Bcr-Abl oncoprotein oligomerisation domain;color=#FF0000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF09036
+22 pfam protein_domain 201581 201640 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621
+22 pfam protein_domain 201941 202126 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621
+22 pfam protein_domain 208994 209101 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621
+22 pfam protein_domain 212118 212178 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621
+22 pfam protein_domain 213667 213719 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621
+22 pfam protein_domain 214220 214312 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621
+22 pfam protein_domain 230954 230999 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168
+22 pfam protein_domain 233127 233224 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168
+22 pfam protein_domain 235610 235741 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168
+22 pfam protein_domain 250010 250018 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168
+22 pfam protein_domain 252302 252422 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620
+22 pfam protein_domain 253473 253607 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620
+22 pfam protein_domain 254554 254659 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620
+22 pfam protein_domain 255138 255228 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620
diff -r 000000000000 -r a24ca22b906e tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
\ No newline at end of file
diff -r 000000000000 -r a24ca22b906e tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jul 27 11:24:44 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+