Merge pull request #6361 from fubar2/sniffles

Sniffles: add test for optional reference history file

tools/sniffles/sniffles.xml

@@ -16,18 +16,21 @@
         <![CDATA[
 ln -f -s '${input}' input.bam &&
 ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
+#if $reference_genome.genome_type_select != "None":
+    #if $reference_genome.genome_type_select == "indexed":
+        ln -f -s '${reference_genome.genome.fields.path}' 'reference.fa' &&
+    #else:
+        ln -f -s '${reference_genome.genome}' 'reference.fa' &&
+    #end if
+#end if
 sniffles
 -t \${GALAXY_SLOTS:-2}
 -i 'input.bam'
 -v '$output'
 ## must set allow-overwrite since the new output vcf file exists
 --allow-overwrite
 #if $reference_genome.genome_type_select != "None":
-    #if $reference_genome.genome_type_select == "indexed":
-        --reference '${reference_genome.genome.fields.path}' 
-    #else:
-        --reference '${reference_genome.genome}' 
-    #end if
+   --reference 'reference.fa' 
 #end if
 ## general_options
     --minsupport '$general_options.minsupport'
@@ -109,6 +112,15 @@ sniffles
             <param name="mosaic" value="--mosaic"/>
             <output name="output" file="expected_outcome5.vcf" lines_diff="4"/>
         </test>
+       <test> <!-- test 6 - reference -->
+            <param name="input" value="reads_region.bam"/>
+            <conditional name="reference_genome">
+                <param name="genome_type_select" value="history"/>
+                <param name="genome" value="humsamp.fa"/>
+                <param name="genome.ext" value="fasta"/>
+            </conditional>
+            <output name="output" file="expected_outcome6.vcf" lines_diff="4"/>
+        </test>
     </tests>
     <help>
         <![CDATA[

tools/sniffles/test-data/expected_outcome3.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/6/outputs/dataset_424b7739-58c9-4942-8a28-964803e1e0e7.dat --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --allow-overwrite"
-##fileDate="2024/09/14 14:16:19"
+##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/6/outputs/dataset_e1aae210-b20c-453b-91cd-8b3e215c9cbf.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/09/26 18:22:15"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

tools/sniffles/test-data/expected_outcome4.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/8/outputs/dataset_b4585ddd-d52d-4087-9461-cb14a87c00d4.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5 --allow-overwrite"
-##fileDate="2024/09/14 14:16:58"
+##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/8/outputs/dataset_ffe443bd-f07b-4644-a417-8bd2aec4cfab.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5"
+##fileDate="2024/09/26 18:22:53"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

tools/sniffles/test-data/expected_outcome5.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/10/outputs/dataset_a28049ec-d2ca-4690-a3ea-fcb59a747505.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic --allow-overwrite"
-##fileDate="2024/09/14 14:17:39"
+##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/10/outputs/dataset_8b1d2d1f-49f4-47d9-8390-b933099f1342.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic"
+##fileDate="2024/09/26 18:23:34"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

tools/sniffles/test-data/expected_outcome6.vcf

@@ -1,6 +1,7 @@
-##fileformat=VCFv4.1
-##source=Sniffles
-##fileDate=20200901:52:19 AMef_minus
+##fileformat=VCFv4.2
+##source=Sniffles2_2.4
+##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/13/outputs/dataset_43c28376-bced-457b-9bc3-79b482047f0a.dat --allow-overwrite --reference /tmp/tmpy46o57ly/files/d/8/7/dataset_d879002d-9f55-45f7-a278-e6c9b6881fe8.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/09/26 18:24:13"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -87,36 +88,58 @@
 ##contig=<ID=GL000192.1,length=547496>
 ##contig=<ID=NC_007605,length=171823>
 ##contig=<ID=hs37d5,length=35477943>
+##ALT=<ID=INS,Description="Insertion">
 ##ALT=<ID=DEL,Description="Deletion">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=INV,Description="Inversion">
-##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries">
-##ALT=<ID=TRA,Description="Translocation">
-##ALT=<ID=INS,Description="Insertion">
-##FILTER=<ID=UNRESOLVED,Description="An insertion that is longer than the read and thus we cannot predict the full size.">
-##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
-##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
-##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
-##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
-##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
-##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
-##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
-##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
-##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read.">
-##INFO=<ID=STRANDS2,Number=4,Type=Integer,Description="alt reads first + ,alt reads first -,alt reads second + ,alt reads second -.">
-##INFO=<ID=REF_strand,Number=.,Type=Integer,Description="plus strand ref, minus strand ref.">
-##INFO=<ID=Strandbias_pval,Number=A,Type=Float,Description="P-value for fisher exact test for strand bias.">
-##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads.">
-##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads.">
-##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads.">
-##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads.">
-##INFO=<ID=SUPTYPE,Number=.,Type=String,Description="Type by which the variant is supported.(SR,AL,NR)">
-##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
-##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
+##ALT=<ID=BND,Description="Breakend; Translocation">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
-##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	input.bam
-21	21492143	0	AAAATATGTTTTAAATTGTTGATGATTTCAAATATTACAGGAATAGAAACTTTAACTTAACACAGAATGATTATCTGGCTTCCTTCTGTAAAATATCTTAAAGGTTAATGTGGATTTGAATTGCACAACATTCCAAATGCTTCTCCCCCTTTAAAAAGAATAGTCTTATCTTTTAAAAAGAATACTCATATCTTTTATTTTTCTTATGCAAGAGCAAAAATAAGGAAAAAATATATTATTCAGGAGAATCATGGCAACAATTTAAGGAAGACAAAACCAGTCTTTAGCAACCAGTATACATATATATCATCTTTTTTTCTGCTTTAGGGTAGGTTGCTTCTATCACCAACCTGTTCCAAATCCTCCTCTTACATGCACCATTAAAACATACTCTTTCAAAAACGAGGTGATAAAATCACAAATATCAATCTATCGTTCAGAAGAAGGTACCTTTATTTTACCTTAAAGGAATTTGATATATAATGGAGAAAAGAAAATTACTTTCT	N	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=21;END=21492649;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=0.572582;Kurtosis_quant_stop=1.417662;SVTYPE=DEL;SUPTYPE=AL,SR;SVLEN=-506;STRANDS=+-;STRANDS2=22,26,22,26;RE=48;REF_strand=19,24;Strandbias_pval=1;AF=0.527473	GT:DR:DV	0/1:43:48
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased">
+##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=GT,Description="Genotype filter">
+##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
+##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
+##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
+##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
+##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
+##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
+##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
+##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
+##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
+##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
+##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
+##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
+##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
+##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
+##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs">
+##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
+##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
+##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
+##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
+##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
+##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
+##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
+##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
+##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
+##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
+##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
+##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
+##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
+##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
+21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48

tools/sniffles/test-data/expected_output.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/2/outputs/dataset_5190dadb-3f7f-474a-a5d2-d0abcdc81344.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --allow-overwrite"
-##fileDate="2024/09/14 14:15:00"
+##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/2/outputs/dataset_b3c7245e-3129-45a7-9a94-f6e837049557.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/09/26 18:20:57"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

tools/sniffles/test-data/expected_output2.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/4/outputs/dataset_5ee6e57f-c129-4b42-81b4-52428800dbe4.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --allow-overwrite"
-##fileDate="2024/09/14 14:15:39"
+##command="/home/ross/miniconda3/envs/[email protected]/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/4/outputs/dataset_f76d3b7c-c912-4135-91ca-b3ca11aa77f2.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/09/26 18:21:36"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>