About input format
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qaac accepts raw PCM, WAV, ALAC, MP3 AAC(LC), and other LPCM formats supported by Apple AudioFile service. Also, qaac can read cue sheets.
When libsndfile-1.dll is installed with qaac, qaac accepts some more PCM formats available with libsndfile. Similarly, libFLAC.dll installation allows FLAC, wavpackdll.dll for WavPack, and tak_deco_lib.dll for TAK.
Basically speaking, input format is automatically detected by qaac. Therefore, you don't have to care or specify what format you are feeding in. However, when you input raw PCM, you have to specify -R (--raw) option, with some other options to tell qaac it's PCM sample format.
--ignorelength is another option concerning inputs. When input is a WAV file and --ignorelength is specified, qaac will ignore the length described in the WAV header (length of the "data" chunk, which holds actual PCM data).
Handling of multiple input, or cuesheet
You can feed multiple input to qaac. Standard wildcards are usable (* and ?). However, you have to be careful. Same options such as encoder settings and tagging options are applied to all encodes.
Basically, each input file is encoded into separated files. Thus, input/ouput relation is 1 to 1. However, story can be different if you feed cuesheet, or if you specify --concat.
When --concat is specified, qaac encodes all input into a single file. In this case, chapter is generated indicating each input track position. Album related tags are fetched from first input file.
Say, you have "01 first track.flac", "02 second track.flac", .... in a directory. When you want to encode these files into a "album image" file (with chapter embedded), you can simply say something like the following:
qaac -V63 --concat *.flac -o output.m4a
When you specify cuesheet as a inputfile, qaac by default encodes each track in the cuesheet into separated file (one file per track). Cuesheet can refer to a single audio file(image), or multiple audio files. However, qaac requires file names in the "FILE" command line being acutual file names. If you have "foo.flac", you cannot have "foo.wav" in your cuesheet.
When --concat is specified, cuesheet tracks are also concatenated into a single output file. Chapter entry for each tracks in cuesheet will be created.
In case of m4a or WAV output, you cannot concatenate multiple files with different sample format (different sample rate, etc). On the other hand, ADTS output will accept such case, and will generate multiple format stream.