Never tried avs2pipemod, but I can confirm that avs2yuv works fine (with YV12, YV16, YV24).
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or I'm doing something wrong.
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Since you don't show the command lines you use, how should anyone know?
Also you did read this from the help of avs2pipemod?
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note1 : in yuv4mpeg2 output mode, RGB input that has 720pix height or more
will be converted to YUV with Rec.709 coefficients instead of Rec.601.
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If you use something with a height > 720pixel and expect the input to be RGB this might cause problems,..
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Or perhaps a way to encode my avs scripts to VP9 video under Wine?
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use a 32bit ffmpeg version compiled for Windows. (64bit if you use 64bit Avisynth)
Cu Selur
Ps.: may be switch to Vapoursynth and drop wine,..