Set start point (--skip=samples/--skip=mm:ss.ms)
Skip over the first number of samples of the input. The alternative form mm:ss.ms can be used to specify minutes, seconds, and fractions of a second. Set duration (--until=[+|-]sample/--until[+|-]mm:ss.ms)
Stop at the given sample number for each input file (the given sample number is not included). The alternative form mm:ss.ms can be used to specify minutes, seconds, and fractions of a second. Relative to the end
If this option is checked the --until point is relative to end of the audio, otherwise the --until point is relative to the --skip point. Seek points (-S #x/--seekpoint=#x/-S #s/--seekpoint=#s)
Include a point or points in a SEEKTABLE. Using #x, # evenly spaced seek points will be added, the first being at sample 0. Using #s, a seekpoint will be added every # seconds. With no -S options, flac defaults to '-S 10s'. Use --no-seektable for no SEEKTABLE (not recommended for normal use). Ogg FLAC output (--ogg)
Generate Ogg FLAC output instead of native FLAC. Ogg FLAC streams are FLAC streams wrapped in an Ogg transport layer. The resulting file should have an '.ogg' extension and will still be decodable by flac. Verify encoded file (-V/--verify)
Verify a correct encoding by decoding the output in parallel and comparing to the original. Sector Align (--sector-align)
Align encoding of multiple CD format WAVE files on sector boundaries. See the HTML documentation for more information. Calculate and store replay gain (--replay-gain)
Calculate ReplayGain values and store in Vorbis comments, similar to vorbisgain. The sample rate must be one of 8, 11.025, 12, 16, 22.05, 24, 32, 44.1, or 48 kHz. Also note that this option may leave a few extra bytes in a PADDING block as the exact size of the tags is not known until all files are processed. Import cue sheet (--cuesheet=filename)
Import the given cuesheet file and store it in a CUESHEET metadata block. Don't add seek points (--no-cued-seekpoints)
A seekpoint will be added for each index point in the cuesheet to the SEEKTABLE unless this option is specified. Add padding (-P length/--padding=length)
Tell the encoder to write a PADDING metadata block of the given length (in bytes) after the STREAMINFO block. This is useful if you plan to tag the file later with an APPLICATION block; instead of having to rewrite the entire file later just to insert your block, you can write directly over the PADDING block. Note that the total length of the PADDING block will be 4 bytes longer than the length given because of the 4 metadata block header bytes. You can force no PADDING block at all to be written with --no-padding. The encoder writes a PADDING block of 4096 bytes by default.
Transcode note: this interface will interpret a padding of 0 bytes as a --no-padding flag. Profile (-N/--compression-level-N/--fast/--best)
These are synonyms for other options (which you can overwrite).

0: Synonymous with -l 0 -b 1152 -r 2,2
1: Synonymous with -l 0 -b 1152 -M -r 2,2
2: Synonymous with -l 0 -b 1152 -m -r 3
3: Synonymous with -l 6 -b 4608 -r 3,3
4: Synonymous with -l 8 -b 4608 -M -r 3,3
5: Synonymous with -l 8 -b 4608 -m -r 3,3
6: Synonymous with -l 8 -b 4608 -m -r 4
7: Synonymous with -l 8 -b 4608 -m -e -r 6
8: Synonymous with -l 12 -b 4608 -m -e -r 6
Fast: Fastest compression. Currently synonymous with -0
Best: Highest compression. Currently synonymous with -8 Exhaustive model search (-e/--exhaustive-model-search)
Do exhaustive model search (expensive!) Max LPC order (-l value/--max-lpc-order=value)
Set the maximum LPC (linear-predictor coefficient) order; 0 means use only the fixed predictors. Quantized LPC precision

0-5 (-q value/--qlp-coeff-precision=value)
Precision of the quantized linear-predictor coefficients (min precisoin is 5, default is 0).
Do exhaustive search (-p/--qlp-coeff-precision-search)
Expensive! Overrides -q value; does nothing if using -l 0 Max residual partition order (-r [min,]max/--rice-partition-order=[min,]max)
Set the max residual partition order (0..16). Default is 3. Min residual partition order (-r [min,]max/--rice-partition-order=[min,]max>)
Set the min residual partition order. Defaults to 0 if unspecified and max is set or to 3 if none is set. Block size

Specify the block size in samples. Default is 1152 for -l 0, else 4608.
Strict (b size/--blocksize=size)
Block size must be one of 192, 576, 1152, 2304, 4608, 256, 512, 1024, 2048, 4096, 8192, 16384, or 32768.
Lax (--lax b size/--lax --blocksize=size)
Allow encoder to generate non-Subset files. The resulting FLAC file may not be streamable or might have trouble being played in all players (especially hardware devices), so you should only use this option in combination with custom encoding options meant for archival. Stereo mode

Mid-Side (-m/--mid-side)
Try mid-side coding for each frame (stereo input only).
Adaptative Mid-Side (-M/--adaptive-mid-side)
Adaptive mid-side coding for all frames (stereo input only).