DB_db_dir  =  ./Database/Fusion/SOAPfuse/GRCh38

DB_wg_soap_ref       =     $(db_dir)/WG_index_soap/genome.fa.index
DB_cytoBand          =     $(db_dir)/cytoBand.txt
DB_trans_soap_ref    =     $(db_dir)/transcript_index_soap/transcript.fa.index
DB_trans_bwa_ref     =     $(db_dir)/transcript_index_bwa/transcript.fa
DB_trans_psl         =     $(db_dir)/transcript.psl
DB_trans_gtf         =     $(db_dir)/Gene_annotation.gtf.gz
DB_gene_psl          =     $(db_dir)/gene.psl
DB_gene_fa           =     $(db_dir)/gene.fa
DB_genefamily        =     $(db_dir)/gene_family/gene_family.brief.txt
DB_blast_homo_list   =     $(db_dir)/blast_homo_gene.m8.gz

PG_pg_dir   =    ./SOAPfuse/SOAPfuse-v1.27/source/bin

PG_soap               =     $(pg_dir)/aln_bin/soap2.21
PG_bwa                =     $(pg_dir)/aln_bin/bwa
PG_blat               =     $(pg_dir)/aln_bin/blat
PG_bwt                =     $(pg_dir)/aln_bin/2bwt-builder2.20
PG_DE_stat            =     $(pg_dir)/DE_statistic
PG_convert            =     $(pg_dir)/convert

PS_ps_dir   =   ./SOAPfuse/SOAPfuse-v1.27/source

PS_s01            =     $(ps_dir)/SOAPfuse-01-alignWG.pl
PS_s02            =     $(ps_dir)/SOAPfuse-02-align_unmap_transcript.pl
PS_s03            =     $(ps_dir)/SOAPfuse-03-align_trim_unmap_transcript.pl
PS_s04            =     $(ps_dir)/SOAPfuse-04-change_SE.pl
PS_s05            =     $(ps_dir)/SOAPfuse-05-candidate.pl
PS_s06            =     $(ps_dir)/SOAPfuse-06-divide_soap_denovo_unmap.pl
PS_s07            =     $(ps_dir)/SOAPfuse-07-junction_seq_deal.pl
PS_s08            =     $(ps_dir)/SOAPfuse-08-final_fusionGene.pl
PS_s09            =     $(ps_dir)/SOAPfuse-09-deeper_analysis.pl


PD_alignWG                   =     $(all_out)/alignWG
PD_align_unmap_Tran          =     $(all_out)/align_unmap_Tran
PD_align_trim_unmap_Tran     =     $(all_out)/align_trim_unmap_Tran
PD_change_SE                 =     $(all_out)/change_SE
PD_candidate                 =     $(all_out)/candidate
PD_denovo_unmap              =     $(all_out)/denovo_unmap
PD_junction_seq              =     $(all_out)/junction_seq
PD_final_fusion_genes        =     $(all_out)/final_fusion_genes


PA_all_somatic_mode        =     no

PA_all_postfix_of_tissue   =     'N:-N;N:-Normal;N:-B;N:-Blood;T:-CA;T:-C;T:-T;T:-Tumor;T:-Cancer'

PA_all_fq_postfix     =     fq.gz

PA_all_process_of_align_software     =     12

PA_all_shortest_length_trim_unmap_to     =     40

PA_all_maximum_genome_loc_trimmed_read_mapped     =     2

PA_all_maximum_genome_loc_intact_read_mapped     =     1

PA_all_intron_len_extend_from_exon_edge     =     100

PA_s02_realign     =     yes

PA_s05_save_genes_name_with_dot     =     no

PA_s05_save_genes_from_same_family     =     yes

PA_s05_amass_control_of_span_reads     =     yes

PA_s05_maximum_fusion_partner_of_one_gene     =     10

PA_s05_the_minimum_span_reads_for_candidate     =     5

PA_s06_save_reads_have_mismatch_around_fusepos     =     yes

PA_s06_number_of_flank_bases_near_read_end_for_filter_mismatch     =     5

PA_s06_the_maximum_mismatch_in_flank_region     =     0

PA_s07_the_minimum_span_reads_for_junction_construction     =     5

PA_s07_extended_bases_near_pe_read_end     =     0

PA_s07_the_min_cons_for_credible_fuse_region     =     0.5

PA_s07_maximum_mismatch_for_align_junction_reads     =     3

PA_s07_flank_bases_around_fuse_point_for_check_mismatch     =     5

PA_s07_maximum_mismatch_in_flank_region     =     0

PA_s07_junc_read_map_both_sides_at_least     =     7

PA_s08_number_of_extend_bases     =     0

PA_s08_insert_control_sup     =   no

PA_s08_min_sum_reads     =     5

PA_s08_min_support_reads_for_both_edge     =     1,1

PA_s08_min_support_reads_for_one_edge_one_internal     =     2,2

PA_s08_min_support_reads_for_both_internal     =     2,2

PA_s08_min_intrachr_distance     =     1000

PA_s08_min_bases_covered_both_sides_around_fuse_point     =     10

PA_s08_only_remain_edge_case     =     no

PA_s09_draw_fusion_expression_svg     =     yes