Added I to cigar matching in restrict_between_reference_positions. Store restricted start and end and original length for use when calculating restricted alignment start and end.
Added I to cigar matching in restrict_between_reference_positions. Store restricted start and end and original length for use when calculating restricted alignment start and end.

ckongEbi/ensembl-compara,kumarsaurabh20/ensembl-compara,etapanari/ensembl-compara,ckongEbi/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,danstaines/ensembl-compara,ckongEbi/ensembl-compara,etapanari/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,dbolser-ebi/ensembl-compara,dbolser-ebi/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,dbolser-ebi/ensembl-compara,danstaines/ensembl-compara