add the option to turn off detect-large-ins which finds half a chromo…

…some insertion.

What does that mean in reads that were from a single subject so 2 independent haplotypes?

tools/sniffles/test-data/expected_outcome3.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/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"
+##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/6/outputs/dataset_85e708bb-74e2-4686-8dca-f0e9404b4e44.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="2024/09/28 23:19:48"
 ##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/__sniffles@2.4/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"
+##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/8/outputs/dataset_76b2ed7a-d091-4613-bda7-505cd86d4277.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="2024/09/28 23:20:28"
 ##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/__sniffles@2.4/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"
+##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/10/outputs/dataset_a9aaaabe-54e2-4f60-9a73-0454076bd7c5.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="2024/09/28 23:21:10"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

tools/sniffles/test-data/expected_outcome6.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/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"
+##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/13/outputs/dataset_93c07e69-9ce4-4394-84c8-8a51cb2e2c89.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/09/28 23:21:51"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

tools/sniffles/test-data/expected_output.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
 ##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/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"
+##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/2/outputs/dataset_c3cc0dff-254a-4e6b-837f-fa8a4db7f051.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --detect-large-ins 0 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/09/28 23:18:28"
 ##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/__sniffles@2.4/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"
+##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/4/outputs/dataset_02006b89-2710-4fcc-9ac1-52a711eebee9.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="2024/09/28 23:19:08"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>