Fix error that occurs when encoding a value greater than 32767 with ‘B, S’ data type in encoding alignment in encoding alignment. #264
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+ Coverage 88.71% 88.87% +0.15%
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Branches 442 442
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+ Hits 5668 5678 +10
+ Misses 279 269 -10
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In encoding alignment options, encoding values greater than 32767 with the 'B, S' data type causes an error.
For example, encoding the following alignment would result in the following error message. Note that the alignment option has the value of '65535' for 'B, S' type.
q006 0 ref 10 60 16M * 0 0 AAAAGGGGTTTTCCCC * XS:B:S,0,32767,65535The reason for error is as follows.
According to BAM format specification, the value of 'B, S' type are encoded with
uint16_t, but the current code was processing withShort/parseShort. Therefore, when encoding values greater than 32767,Short/parseShortreturns an error.This PR solves this problem by removing
Short/parseShortand usinglsb/write-ushort. This PR also adds tests to convert SAM/BAM file that contains the alignments with 'B, S' type data.