<filename>SVassembly/__init__.py
from SVassembly import bedpe2window_f
from bedpe2window_f import bedpe2window

from SVassembly import get_shared_bcs_f
from get_shared_bcs_f import get_shared_bcs

from SVassembly import assign_sv_haps_f
from assign_sv_haps_f import assign_sv_haps

from SVassembly import count_bcs_f
from count_bcs_f import count_bcs #can't have "-" 

from SVassembly import map_to_genome_f
from map_to_genome_f import map_to_genome

from SVassembly import extract_reads_2_0_new
from extract_reads_2_0_new import extract_readsv2_0_new  #LR v2.0

from SVassembly import extract_reads_2_0_old
from extract_reads_2_0_old import extract_readsv2_0_old  #LR v2.0

from SVassembly import extract_reads_by_barcode_2_1_new #uncomment these
from extract_reads_by_barcode_2_1_new import extract_readsv2_1_new #LR v2.1

from SVassembly import extract_reads_by_barcode_2_1_old #uncomment these
from extract_reads_by_barcode_2_1_old import extract_readsv2_1_old #LR v2.1

from SVassembly import InterestingContigs
from InterestingContigs import interestingContigs

from SVassembly import filt_svs
from filt_svs import filter_svs

from SVassembly import align
from align import mappyAlign

from SVassembly import mappy_contig_eval
from mappy_contig_eval import interesting_contigs_mappy

#from SVassembly import phase_svs
#from phase_svs import phase

#from SVassembly import plot_bcs_across_bkpts #this is an R file

from SVassembly import plot_bcs_across_bkpts
from plot_bcs_across_bkpts import plot_bcs_bkpt

<filename>SVassembly/__init__.py
from SVassembly import bedpe2window_f
from bedpe2window_f import bedpe2window

from SVassembly import get_shared_bcs_f
from get_shared_bcs_f import get_shared_bcs

from SVassembly import assign_sv_haps_f
from assign_sv_haps_f import assign_sv_haps

from SVassembly import count_bcs_f
from count_bcs_f import count_bcs #can't have "-" 

from SVassembly import map_to_genome_f
from map_to_genome_f import map_to_genome

from SVassembly import extract_reads_2_0_new
from extract_reads_2_0_new import extract_readsv2_0_new  #LR v2.0

from SVassembly import extract_reads_2_0_old
from extract_reads_2_0_old import extract_readsv2_0_old  #LR v2.0

from SVassembly import extract_reads_by_barcode_2_1_new #uncomment these
from extract_reads_by_barcode_2_1_new import extract_readsv2_1_new #LR v2.1

from SVassembly import extract_reads_by_barcode_2_1_old #uncomment these
from extract_reads_by_barcode_2_1_old import extract_readsv2_1_old #LR v2.1

from SVassembly import InterestingContigs
from InterestingContigs import interestingContigs

from SVassembly import filt_svs
from filt_svs import filter_svs

from SVassembly import align
from align import mappyAlign

from SVassembly import mappy_contig_eval
from mappy_contig_eval import interesting_contigs_mappy

#from SVassembly import phase_svs
#from phase_svs import phase

#from SVassembly import plot_bcs_across_bkpts #this is an R file

from SVassembly import plot_bcs_across_bkpts
from plot_bcs_across_bkpts import plot_bcs_bkpt

#can't have "-" #LR v2.0 #LR v2.0 #uncomment these #LR v2.1 #uncomment these #LR v2.1 #from SVassembly import phase_svs #from phase_svs import phase #from SVassembly import plot_bcs_across_bkpts #this is an R file