print a help message
    svdb  --build --help  
Construct a database, from a set of vcf files:
    svdb --build --vcf sample1.vcf sample2.vcf sample3.vcf
construct a database from vcf files stored in a folder
    svdb --build --folder SV_analysis_folder/
    
optional arguments:
    -h, --help                      show this help message and exit

    --files [FILES [FILES ...]]      create a db using the specified vcf files(cannot be
                                     used with --folder)
                    
    --folder FOLDER                  create a db using all the vcf files in the folders
    
    --prefix PREFIX                  the prefix of the output file, default = SVDB

print a help message
    svdb  --export --help  
Export the variants of the database database.db:
    svdb --export --db database.db

optional arguments:
    --no_merge            skip the merging of variants, print all variants in the db to a vcf file

     --ci                  overides overlap and bnd_distance,determine hits based on the confidence interval of the position of the variants(0 if no CIPOS or CIEND is vailable)

      --bnd_distance BND_DISTANCE  the maximum distance between two similar precise breakpoints(default = 2500)

     --overlap OVERLAP     the overlap required to merge two events(0 means anything that touches will be merged, 1 means that two events must be identical to be merged), default = 0.8

     --DBSCAN              use dbscan to cluster the variants, overides the overlap based clustering algoritm

      --epsilon EPSILON     used together with --DBSCAN; sets the epsilon paramter(default = 500bp)

      --min_pts MIN_PTS     used together with 1--DBSCAN; sets the min_pts parameter(default = 2

      --prefix PREFIX       the prefix of the output file, default = same as input


      --memory              load the database into memory: increases the memory requirements, but lowers the time consumption

print a help message
    svdb --hist --help
Create histograms of different sizes, and compute their efficiency:
    svdb --hist --sample_hist -folder input
Create a similarity matrix of the selected sampes:
    svdb --hist --similarity_matrix -folder input

optional arguments:

    -h, --help                      show this help message and exit
    
    --files [FILES [FILES ...]]     input vcf files(cannot be used with folder)
     
    --k [K [K ...]]                 the sizes of the sampled databases
                                    default = n=10*i < samples(used with sample_hist)
    
    --n N                           the number of iterations,default=100(used with sample_hist)

    --bnd_distance BND_DISTANCE     the maximum distance between two similar precise
                                    breakpoints(default = 10000)
                                    
    --overlap OVERLAP               the overlap required to merge two events(0 means
                                    anything that touches will be merged, 1 means that two
                                    events must be identical to be merged), default = 0.6
    
    --ci                            overides overlap and bnd_distance,determine hits based
                                    on the confidence interval of the position of the
                                    variants(0 if no CIPOS or CIEND is vailable)

print a help message
   svdb --query --help
Query a structural variant database, using a vcf file as query:
    svdb --query --query_vcf patient1.vcf --db control_db.vcf
The vcf may be a exported SVDB database or a multismple vcf. The frequencies used for each variant is computed from the format fields of the vcf.
The SVDB sqlite database may also be used for querying:
    svdb --query --query_vcf patient1.vcf --sqdb control_db.db

optional arguments:

	-h, --help            show this help message and exit
	--db DB               path to a SVDB db vcf
	--sqdb SQDB           path to a SVDB sqlite db
	--hit_tag HIT_TAG     the tag used to describe the number of hits within the info field of the output vcf(default=OCC)
	--frequency_tag FREQUENCY_TAG the tag used to describe the frequency of the variant(defualt=FRQ)
	--prefix PREFIX       the prefix of the output file, default = print to stdout --bnd_distance BND_DISTANCE the maximum distance between the breakpoints of two variantsbreakpoints(default = 10000)
	--overlap OVERLAP     the overlap threshold for deciding if two variants are similar(0 means anything that touches will be merged, 1 means that two events must be identical to be merged), default = 0.6
	--memory              load the database into memory: increases the memory requirements, but lowers the time consumption(may only be used with sqdb)
	--no_var              count overlaping variants of different type as hits in the db
	--invert              invert the sorting order so that high frequency samples are present on top of the output vcf
	--ci				  overides overlap and bnd_distance,determine hits based on the confidence interval of the position fo the variants(0 if no CIPOS or CIEND is vailable)

print a help message:
   python SVDB.py --merge --help
merge vcf files:
    svdb --merge --vcf patient1_lumpy.vcf patient1_cnvnator.vcf patient1_TIDDIT.vcf > patient1_merged_callers.vcf

Similar variants will be merged, and presented according to the order of the input vcf files. I.e If lumpy and cnvnator calls the same variant in the top example,
the variant will be printed as the lumpy call. In most cases, the order should be set according to the accuracy or detail of the info field of the different callers.
The order could also be set using the --priority flag:
    svdb --merge --vcf patient1_lumpy.vcf:one patient1_cnvnator.vcf:2 patient1_TIDDIT.vcf:tiddit --priority tiddit,2,one > patient1_merged_callers.vcf

In this example, tiddit will have the highest order, cnvnator second etc.


optional arguments:
    -h, --help                      show this help message and exit
    
    --bnd_distance BND_DISTANCE     the maximum distance between two similar precise breakpoints
                                    (default = 10000)
                    
    --overlap OVERLAP               the overlap required to merge two events(0 means
                                    anything that touches will be merged, 1 means that two
                                    events must be identical to be merged), default = 0.6


    --priority                      prioritise the input vcf files
                          
    --ci                            overides overlap and bnd_distance,determine hits based
                                    on the confidence interval of the position fo the
                                    variants(0 if no CIPOS or CIEND is vailable)
                                    
    --no_intra                       no merging of variants within the same vcf
    
    --no_var                        variants of different type will be merged
    
    --pass_only                     merge only variants labeled PASS