ó £žbc@s´ddlmZddlmZmZddlmZmZmZm Z ddl m Z m Z m Z ddlmZd„Zd d„Zd„Zd „Zd „Zd d „Zd S( iÿÿÿÿ(t defaultdict(t fastaparsertqconfig(tprocess_misassembled_contigt IndelsInfot find_all_svt Misassembly(tget_best_aligns_setstget_used_indexestscore_single_align(tref_labels_by_chromosomescCs/t|}||jtjƒ|j|ƒdS(N(R tappendRtPOSSIBLE_MISASSEMBLIEStadd(treftmisassemblies_by_reftrefs_with_translocationstcur_ref((sQ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/ca_utils/analyze_contigs.pytadd_potential_misassemblys c Cs€|}t|ƒ}|jdƒ}d}||tjkr|d}t|j||ƒ|r||d7}t|j||ƒq|n|S(NtNii(tlentcountRtunaligned_part_sizeRR( tseqtalignRRt second_aligntunaligned_partt unaligned_lentcount_nstpossible_misassemblies((sQ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/ca_utils/analyze_contigs.pytprocess_unaligned_parts  cCsMd}d}tƒ}x‘t|ƒD]ƒ\} } | jƒ|dkr™| dkr^|| dnd} t||| jƒ!| ||d| ƒ} || 7}n| jƒ}q"W||krât|||!|d||ƒ} || 7}n|sìdS|jtjƒ|j tj g|ƒx"|D]} || jtjƒqW|j d|ƒdS(NiiRiÿÿÿÿsd It can contain up to %d interspecies translocations (will be reported as Possible Misassemblies). 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