gqt query crashes with large annotations (fix inside)

[jpiper]

I have a BCF file, and one line has a very large annotation field (2 million characters - almost 10MB), which crashes gqt query.

This stems from the conservative 1MiB output_buffer_main_buf_size as defined in src/output_buffer.c, so this issue can can be solved by increasing this and recompiling.

I'm wondering if you think it's worth increasing the buffer size or allowing for dynamic growth or automatic flushing of the output buffer?

If not, at least this issue will help other people solve this issue if they run into it :)

[ryanlayer]

Thanks for finding this. I think it is a good idea to increase this buffer and I will in the next release.

On Mon, Jul 4, 2016 at 11:28 PM, Jason Piper [email protected] wrote:

I have a BCF file, and one line has a very large annotation field (2 million characters - almost 10MB), which crashes gqt query.

This stems from the conservative 1MiB output_buffer_main_buf_size as defined in src/output_buffer.c, so this issue can can be solved by increasing this and recompiling.

I'm wondering if you think it's worth increasing the buffer size or allowing for dynamic growth or automatic flushing of the output buffer?

If not, at least this issue will help other people solve this issue if they run into it :)

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Ryan Layer