U 7gb;@s4dZddlmZddlZddZddZd d ZdS) z Utilities for VCF files. ) BgzfBlocksNcCs|dkr dSt|d}|dd}|dkrN|ddtj|dddS|d krv|dtd d t|DSt|d}|dtj| SdS) Nrrbslittle) byteorderscSsg|] }|dqS).0ir r (lib/python3.8/site-packages/vcf/utils.py sz)get_uncompressed_size..) openreadseekint from_bytessumrosSEEK_ENDtell)filepathZdeviceZ magic_4bytesr r rget_uncompressed_sizes    rc /sFd|kr|dnddg|D]6}zt|Wq"tk rVdYq"Xq"dtddDrBtfdd tD}fd dt|D}t|rt|n t|t fd dt| Dfd dt t DVD]:}zt|||<Wntk r:d|<YnXqq^dS) a Simultaneously iteratate over two or more VCF readers. For each genomic position with a variant, return a list of size equal to the number of VCF readers. This list contains the VCF record from readers that have this variant, and None for readers that don't have it. The caller must make sure that inputs are sorted in the same way and use the same reference otherwise behaviour is undefined. Args: vcf_record_sort_key: function that takes a VCF record and returns a tuple that can be used as a key for comparing and sorting VCF records across all readers. This tuple defines what it means for two variants to be equal (eg. whether it's only their position or also their allele values), and implicitly determines the chromosome ordering since the tuple's 1st element is typically the chromosome name (or calculated from it). Zvcf_record_sort_keycSs |j|jfSN)ZCHROMZPOS)rr r r2zwalk_together..NrcSsg|] }|dk qSrr )r rr r rr<sz!walk_together..c3s&|]\}}|dk r||fVqdSrr )r rr)get_keyr r =sz walk_together..cs g|]}|ddkr|qS)rr )r kmin_kr rr?scsg|]\}}|kr|qSr r )r rr"r#r rrGscs g|]}|kr|ndqSrr r ) min_k_idxsnextsr rrHs) appendnext StopIterationanydict enumeratelistvaluesminsetitemsrangelen)ZreaderskwargsreaderZ next_idx_to_kZkeys_with_prev_contigrr )r r$r%r&r walk_togethers6      r6cs|sgSdd|D}t|}t|}t|dkr6|St|ddD]:\}||krFdkrj|Sfdd|DSqFfdd|DS) a_ Trim a list of sequences by removing the longest common suffix while leaving all of them at least one character in length. Standard convention with VCF is to place an indel at the left-most position, but some tools add additional context to the right of the sequences (e.g. samtools). These common suffixes are undesirable when comparing variants, for example in variant databases. >>> trim_common_suffix('TATATATA', 'TATATA') ['TAT', 'T'] >>> trim_common_suffix('ACCCCC', 'ACCCCCCCC', 'ACCCCCCC', 'ACCCCCCCCC') ['A', 'ACCC', 'ACC', 'ACCCC'] cSsg|]}|dddqS)Nr r seqr r rrdsz&trim_common_suffix..rNr7rcsg|]}|d qSrr r8rr rrmscsg|]}|dd qS)Nrr r8r:r rrns)r/maxr3r,) sequencesZreversesZrev_minZrev_maxcr r:rtrim_common_suffixQs  r>)__doc__Zbgzfrrrr6r>r r r rs  4