[compiler] read sequence list fully in tabix parser - #10733
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CHANGELOG: Fix a bug in tabix parsing when the size of the list of all sequences is large BGZipInput stream will (validly) only copy to the end of its internal buffer on a call to `int read(byte[] b, int off, int len)`. The internal buffer is at most 64k, so the single `read` call when reading the sequences could often not read the entire list. Replacing it with readFully solves the issue.
tpoterba
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Jul 30, 2021
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nice! That's dastardly.
daniel-goldstein
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Aug 3, 2021
CHANGELOG: Fix a bug in tabix parsing when the size of the list of all sequences is large BGZipInput stream will (validly) only copy to the end of its internal buffer on a call to `int read(byte[] b, int off, int len)`. The internal buffer is at most 64k, so the single `read` call when reading the sequences could often not read the entire list. Replacing it with readFully solves the issue.
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CHANGELOG: Fix a bug in tabix parsing when the size of the list of all sequences is large
BGZipInput stream will (validly) only copy to the end of its internal
buffer on a call to
int read(byte[] b, int off, int len). The internalbuffer is at most 64k, so the single
readcall when reading thesequences could often not read the entire list. Replacing it with
readFully solves the issue.