The Third Manual input format is the SIMPLE_BGA file which File format makes it easy to enter all the pins from a BGA quickly. It is easiet easiest to create this in a spreadsheet program, and the pins can often be copied directly from a pdf.
The pin_names are entered into the rows and columns of the BGA, and then a section follows where the pin_types for a matching name are defined.
The image below shows the SIMPLE_BGA format for an LTM4600 Power module which is laid out in rows and columns with many empty pin slots. It has 23 columns and 16 Rows [A-T with no I, O or S]
The COLUMN numbers are defined across the top row with the !COL directive in the first Column. The Row Letters are then entered as the first column of each row below it.
The PinNames for each row/col are entered in the matrix and Part_Builder automatically tracks the pin numbers. So in Figure 4 below, pin voset gets resolved to A21 while PGOOD gets resolved to J23
Underneath the pin matrix the user enters the may optionally provide PIN_TYPE_DEFS to inform partBuilder give PartBuilder the pin types for each pin name. The PIN_TYPE_DEFS work using pin name matching, so one definition can apply to many pins. For example PGND=GND says that any pin containing PGND in the name is a POWER pin, and voset=INPUT says that the voset pin is an input, and PGOOD=output says that Pgood is an output. When part_builder PartBuilder runs, it must be able to find a pin type definition for every pin, and it will report any pins that it cannot find a definition for. 
The PIN_OVERRIDE_TYPE file can also be used to provide this information so that the user doesn't have to edit the spreadsheet information they may have obtained from a vendor PDF file. More information on the PIN_OVERRIDE_TYPE file can be found at this link PIN_TYPE_OVRD File
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