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Work out difference between query_length and infer_query_length #8

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zyxue opened this issue Jul 13, 2018 · 1 comment

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zyxue commented Jul 13, 2018

query_length
http://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.query_length

infer_query_length
http://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.infer_query_length

Owner Author

zyxue commented Jul 13, 2018

Insertion (I38) and softclip (S) don't seem to make a difference

(Pdb) contig.query_name
'A1.R26257'
(Pdb) contig.cigarstring
'241M96N77M1I38M13S'
(Pdb) contig.query_length
370
(Pdb) contig.infer_query_length()
370
(Pdb) contig.infer_query_length(always=True)
370

hardclip will

(Pdb) contig.query_name
'A0.R100625'
(Pdb) contig.cigarstring
'138S23M35539N111M36422N13M1D12M3I849M2185H'
(Pdb) contig.query_length
1149
(Pdb) contig.infer_query_length()
1149
(Pdb) contig.infer_query_length(always=True)
3334
(Pdb) 1149 + 2185 # (hardclip)
3334

zyxue closed this as completed

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