diff --git a/README b/README index be4d9f418d506a5dfa2521e96542d47c5f586da9..63dfebea02b43fbb8612a572d02b594c241d1c90 100644 --- a/README +++ b/README @@ -33,6 +33,13 @@ git pull origin master - Python 3 - BioPython for Python3 +For build_xls_results script, these python3 modules are required: + - yalm + - pybedtools + - pysam + - vcf + - xslxwriter + ################ # How to use ? # diff --git a/svreader/__init__.py b/svreader/__init__.py index 1bc14d6cf76d053edb71734edcc708528ce300ce..6a34ff6d75302ea8619664babd89527f4eeeef68 100644 --- a/svreader/__init__.py +++ b/svreader/__init__.py @@ -1,4 +1,3 @@ - import os import re @@ -173,10 +172,8 @@ class SVReader(object): return (abs(record.sv_len) >= minlen and abs(record.sv_len) <= maxlen) def SpecificFilterPass(self,record): - return True - - #def merging(self,vcf_records, overlap_cutoff = 0.5, left_precision = 200, right_precision = 200): - # return mergeSV(vcf_records, self.getOrderedSamples(), overlap_cutoff, left_precision, right_precision, self.tool_name) + return True + class SVWriter(object): def __init__(self, file_name, tool_name, template_reader):