o VA(f"@s<dZddlZddlZeddZeddZddZid d d d d d d d d d dd dd dd dddddddddddddddd d!d"d#d$d%d&d'Zid d d dd dd dddddddddddddd dd"dd#d(d$d(d%d)d&d)Zd*d+Z d,d-Z d.d/Z d0d1Z d2d3Z dS)4z>Tools for working with files in the samtools pileup -c format.NPileupSubstitution) chromosomeposreference_basegenotypeconsensus_quality snp_qualitymapping_qualitycoverage read_basesbase_qualities PileupIndel) rrrrrrr r Z first_alleleZ second_alleleZ reads_firstZ reads_secondZ reads_diffc cstddttttttttf }tddtttttttttttf }|D]K}|dd}|ddkrPztdd t||DVWq"tyOtd |wztd d t||DVWq"tymtd |wdS) a/iterate over ``samtools pileup -c`` formatted file. *infile* can be any iterator over a lines. The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution` or :class:`pysam.Pileup.PileupIndel`. .. note:: The parser converts to 0-based coordinates cS t|dSNintxr,lib/python3.10/site-packages/pysam/Pileup.py0 ziterate..cSrrrrrrrr2rN*cSg|]\}}||qSrr.0ryrrr 9ziterate..zparsing error in line: `%s`cSrrrrrrrr >r!) strrsplitr zip TypeErrorpysamZ SamtoolsErrorr)infileZ conv_substZ conv_indellinedrrriterate#s*    r*ACGTZAAZCCZGGZTTZUUUZAGrZGARZCTrZTCYZACmZCAMGTkZTGKsSwW)CGZGCATZTAr<r=cCs t|S)zencode genotypes like GG, GA into a one-letter code. The returned code is lower case if code[0] < code[1], otherwise it is uppercase. )ENCODE_GENOTYPEuppercoderrrencodeGenotype^s rBcCst|S)z|decode single letter genotypes like m, M into two letters. This is the reverse operation to :meth:`encodeGenotype`. )DECODE_GENOTYPEr@rrrdecodeGenotypefsrDc sddddfdd}gg}}d}|D]$}z |||\}}Wn ty-Ynw|||dkr<||qd }|rDttt|d ksPJd |d }d |}||fS)z*translate indel from vcf to pileup format.cSsLtt|t|}t|D]}||||kr|d|Sq |d|S)z'get common prefix of strings s1 and s2.Nminlenranges1s2nrrrr getPrefixqs   z0translateIndelGenotypeFromVCF..getPrefixcSsptt|t|}|d|dkrdStd| ddD]}||||kr0||ddSq|| dS)z&get common sufix of strings s1 and s2.rrNrErIrrr getSuffixysz0translateIndelGenotypeFromVCF..getSuffixcs||krdSt|t|krg||r#d|t|dt|dfS||r5d|dt| dfS||}||}t|t|t|}|dkrRtd|t|t|| t|dfSt|t|kr||rd|t|dt|dfS||rd|dt|dfS||}||}t|t|t|}|dkrtd|t|t|| t|fSJd)N)rrz-%srrrz+%szsnp?)rG startswithendswith ValueError)variantrefprefixsuffixZsharedrMrPrr getGenotypes2     *     &z2translateIndelGenotypeFromVCF..getGenotypeTrFrzmultiple offsets for indelr/)rSappendrGsetjoin) Z vcf_genotypesrUrY genotypesZoffsetsZis_errorrTgoffsetrrXrtranslateIndelGenotypeFromVCFms, )    racs8|j}|j}|j}|g|j||}|d}t|dkr%tdt||d}|ddkr1dSfdd|D}|d dgd}}|jd dgd} |d d} t|dksgt d d|jDdkrt ||\} } t ||| d | ||| | | dt| ddd St d |} d} d}t|||| ||| | | | S)z$convert vcf record to pileup record.r5rz%only single genotype per position, %sr.Ncs g|] }|dkrt|qS)rZrrrZallellesrrr s zvcf2pileup..ZGQZMQZDPcSsg|]}t|qSr)rGrcrrrr srrCrBrDrarlrprrrrs       Y :