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while (<STDIN>) {
# Samfile refactoring
s/Samfile/AlignmentFile/g;
# AlignedRead refactoring
s/AlignedRead/AlignedSegment/g;
# Do these patterns first as they match
# the new names
s/\.query/\.query_alignment_sequence/g;
s/\.positions/\.getReferencePositions()/g;
# Tabixfile, etc
s/Tabixfile/TabixFile/g;
s/Fastafile/FastaFile/g;
s/Fastqfile/FastqFile/g;
# basic attributes
s/\.qname/\.query_name/g;
s/\.tid/\.reference_id/g;
s/\.pos/\.reference_start/g;
s/\.mapq/\.mapping_quality/g;
s/\.rnext/\.next_reference_id/g;
s/\.pnext/\.next_reference_start/g;
s/\.tlen/\.query_length/g;
s/\.seq/\.query_sequence/g;
if (/\.qual =/) {
s/([[\].0-9a-zA-Z]*)\.qual = (\S*)/$1.query_qualities = pysam.fromQualityString($2)/g;
} else {
s/([[\].0-9a-zA-Z]*)\.qual/pysam.toQualityString($1\.query_qualities)/g;
}
s/\.alen/\.reference_length/g;
s/\.aend/\.reference_end/g;
s/\.rlen/\.query_alignment_length/g;
s/([[\].0-9a-zA-Z]*)\.qqual/pysam.toQualityString($1\.query_alignment_qualities)/g;
s/\.qstart/\.query_alignment_start/g;
s/\.qend/\.query_alignment_end/g;
s/\.qlen/\.query_alignment_length/g;
s/\.mrnm/\.next_reference_id/g;
s/\.rnext/\.next_reference_id/g;
s/\.mpos/\.next_reference_start/g;
s/\.rname/\.reference_id/g;
s/\.isize/\.query_length/g;
s/\.cigar/\.cigartuples/g unless (/\.cigarstring/);
s/\.blocks/\.getBlocks()/g;
s/\.aligned_pairs/\.getAlignedPairs()/g;
s/\.inferred_length/\.getInferredQueryLength()/g;
s/\.overlap()/\.getOverlap()/g;
# PileupProxy
s/\.n([^a-zA-Z])/\.nsegments$1/g;
# if (/\.mrnm/ || /\.rnext/ || /\.mpos/ || /\.rname/)
# {
# warn "Deprecated tag $& at line $.\n";
# }
print;
}
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