ffmpeg – VOB to flv + movs

ls /cygdrive/k/VIDEO_TS/VTS_01_*.VOB| while read line; do in=`echo $line|cut -d”/” -f5 `; ffmpeg -i $line -vcodec libx264 -pass 1 -vpre fastfirstpass -ar 44100 -ab 128k -b 2M -deinterlace -y /cygdrive/e/_BERIVAN_OKTAY_DUGUN/DVD3/$in.flv;done

then, once you have the video as h264, no reencoding is required for movs:
use ffmpeg -i NAME -vcodec copy -acodec copy NAME.mov


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