change.log

__author__ = 'xutengfei'
__author_email__ = 'xutengfei1@genomics.cn
Fuc:
         1: data preprocessing
	 2：crate index
	 3: bwa
	 4: snp and indel calling by GATK+ freebayes + bcftools
	 5: concat and merge vcf
	 6: cnv calling by cnvcaller
	 7: sv calling by breakdancer and lumpy
	 8: find_gene
	 9: vcf stat
	10: merge sv
Require python3.x
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Click                              7.0
pathlib                          2.3.0
matplotlib	       	         3.0.0+
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changelog:
	1: modified the file reading method
	2: bug that -i parameter must be positive in snpcall subcommand has been corrected.
	3: change file wirting way
	4: prompt for successful modification
	5: rm sam in correct folder
	6：modified selectsnp command in GATK
v1.0
    1:change the parameter of cutadapt -p 30,30 to -p 20,20
    2:change the parameter of sickle -p 30, -l 30 to -p 20, -l 50
	3:change folder name from lower to upper and number
	4:add re.IGNORECASE
	5:replace grep "XT:A:U" to -q 30 in bwa
	6:fix '/' end in refer genome path
	7:split bwa output work.sh
	8:Modify variable naming
v1.1
	1:The robustness of using relative paths is increased
v1.2
	1:add GATK home dict
	2:create realign bam file list
v1.3
	1:Now user can customize the software path
	2:find_gene in GWAS's SNP
v1.4
	1: fix vcf_merge and bam_merge
	2: beagle add option ne=1000 (effective population size) 
	3: now can selcet cutting adapter or not
v1.4.1
	1: Abandon picard's sortsam module
v1.4.2
	1:Using toml for Environment Configuration
v1.4.3
	1:use the latest version picard,replaced some command of picard
v1.5
	1:could use bwa-mem2
	2:optimize snpcall process
v1.5.1
	1:sort 04.Realign work.sh
	2:use sambamba to sort bam
v1.6
	1:delete bam_merge
	2:add bam_stat
	3:add indel detection
	4:add cnv detection

v1.6.1
	1: add the fuction of vcf_stat
v1.6.2
	1: Not using toml
v1.6.3
	1:add sv detection
v1.6.4
	1:add sv merge
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