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I was hoping gdalwarp could merge and crop MODIS tiff images such that the original cell size and alignment is maintained. I tried the command below, but cell size is off slightly and cell alignment is offset from 10 to 100 meters.

gdalwarp -cutline basins.shp -crop_to_cutline input1.tif input2.tif input3.tif outputmergeclip.tif

I tried setting -tr to the source cell size, -te to the extent of the shapefile snapped to the source grid cell alignment and -tap, but these didn't make any change in the result. Am I interpreting the options incorrectly? Am I on the wrong track with gdalwarp?

I'm scripting this in Python and relatively new to both python(2.7) and gdal(1.9.2).

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