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I am looking for a audio/video muxer which can work without user intervention like in a command line or API. I tried Avidemux but it seems to be finicky. Sometimes it works and many times not.

Is there any other tool which just works every time? I don't mind if it's commercial.

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What OS are you using? – micke Mar 26 '12 at 17:19
I am using Windows 7 – Tony_Henrich Mar 26 '12 at 17:41

Try a windows build of FFmpeg or even WinFF.
FFmpeg doesn't have the video editing features of Avidemux but it sounds like you don't need them anyway.

Here's a good howto document to get you started.

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Try MLT framework

It exposes API in C++,Python. It also has an CLI called melt which can do almost all Non-Linear editing jobs

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