abif cheatsheet

Every export of @deckyard/abif. Guides are listed in the introduction.

jennifer

import "@deckyard/abif/" as abif;

Every failure is Error{kind: "abif"}, except that open passes on what fs.readBytes throws. An f argument is a File; a tag is a name (four characters, such as DATA) and a number.

Constants

Constant	Value	Meaning
`MAX_ENTRIES`	`65536`	the most directory entries `parse` accepts; real files have 20 to 200

Files and the directory

Function	Returns	Does
`parse(data)`	`File`	check the header and every directory entry against `data`, then index them
`open(path)`	`File`	`parse` of a file read from disk
`tags(f)`	`list of string`	every tag as `NAME` + number (`DATA9`, `PBAS2`), in file order
`has(f, name, number)`	`bool`	whether the directory lists a tag
`entries(f)`	`list of Entry`	the directory, in file order
`entry(f, name, number)`	`Entry`	a tag's directory entry; throws when it is missing
`raw(f, name, number)`	`bytes`	a tag's data, whatever its type

Values

Function	Returns	Does
`tag(f, name, number)`	`Value`	a tag decoded by its element type
`text(f, name, number)`	`string`	a `pString`, `cString` or `char` tag as UTF-8 text, untrimmed
`ints(f, name, number)`	`list of int`	a `byte`, `char` (0 to 255), `word`, `short` or `long` tag
`floats(f, name, number)`	`list of float`	a `float` or `double` tag
`typeName(elementType)`	`string`	`short`, `pString`, `user`, ...; `unknown` for a code the specification does not name

The run

Function	Returns	Does
`rawTrace(f, dye)`	`list of int`	the raw signal of a dye: `DATA` 1 to 4, then 105 and up
`analysedTrace(f, dye)`	`list of int`	the analysed signal: `DATA` 9 to 12, then 205 and up
`dyes(f)`	`list of Dye`	the dyes with names and wavelengths (`Dye#`, `DyeN`, `DyeW`)
`calls(f)`	`Calls`	bases, qualities and peak locations as called (`PBAS`, `PCON`, `PLOC` 2)
`editedCalls(f)`	`Calls`	the same as edited by a user (number 1)
`info(f)`	`Info`	sample, well, instrument, run times and other metadata

Types

`File`

The directory is one list per Entry field, so a File holds none of the deck's structs and is not rebuilt each time it is passed to the deck; entries and entry return Entry values.

Field	Meaning
`version as int`	the format version: 101 in `.ab1` and `.fsa`, 300 in 3500 HID files
`names as list of string`	each entry's tag name, in file order
`numbers as list of int`	each entry's tag number
`elementTypes as list of int`	each entry's element type
`elementSizes as list of int`	each entry's element size
`counts as list of int`	each entry's element count
`dataSizes as list of int`	each entry's data size
`offsets as list of int`	each entry's data offset
`index as map of string to int`	the position of each tag in those lists, keyed `NAME` + number
`data as bytes`	the whole file

`Entry`

Field	Meaning
`name as string`	the tag name, such as `DATA`
`number as int`	the tag number
`elementType as int`	the element type code
`elementSize as int`	bytes per element
`count as int`	the number of elements
`dataSize as int`	bytes of data, `count * elementSize`
`offset as int`	where the data starts in the file; 4 bytes or less sit in the entry itself

`Value`

Variant	Payload	Holds
`Ints`	`values` (`list of int`)	`byte`, `word`, `short`, `long` elements
`Floats`	`values` (`list of float`)	`float`, `double` elements
`Chars`	`data` (`bytes`)	`char` elements: text such as `PBAS`, or numbers such as `PCON`
`Text`	`value` (`string`)	a `pString` or `cString`
`Dates`	`values` (`list of Date`)	`date` elements
`Times`	`values` (`list of Time`)	`time` elements
`Thumbs`	`values` (`list of Thumb`)	`thumb` elements
`Bools`	`values` (`list of bool`)	`bool` elements
`Raw`	`elementType` (`int`), `data` (`bytes`)	any other type: user types, obsolete ones, encrypted HID types

`Date`

Field	Meaning
`year as int`	the year
`month as int`	the month as stored
`day as int`	the day as stored

`Time`

Field	Meaning
`hour as int`	the hour as stored
`minute as int`	the minute as stored
`second as int`	the second as stored
`hundredths as int`	hundredths of a second as stored; some instruments write values above 99

`Thumb`

Field	Meaning
`d as int`	the first 32-bit field
`u as int`	the second 32-bit field
`c as int`	the first byte field
`n as int`	the second byte field

`Dye`

Field	Meaning
`number as int`	the dye number, also its trace's
`name as string`	its name, such as `6-FAM`; `""` when absent or encrypted
`wavelength as int`	its emission wavelength in nm; 0 when absent or not one integer

`Calls`

Field	Meaning
`bases as string`	the called bases, IUPAC codes
`qualities as list of int`	one quality value per base, 0 to 255; empty when the file has none
`peaks as list of int`	one peak location (a scan number) per base; empty when the file has none

`Info`

Text fields have trailing spaces and NULs removed and are "" when the file does not have them as text.

Field	Meaning
`sample as string`	the sample name (`SMPL`)
`well as string`	the well, such as `B9` (`TUBE`)
`lane as int`	the capillary or lane (`LANE`); 0 when absent or not one integer
`instrument as string`	the instrument name and serial number (`MCHN`)
`model as string`	the instrument model, such as `3730` (`MODL`)
`runName as string`	the run name (`RunN`)
`runModule as string`	the run module (`RMdN`)
`dyeSet as string`	the dye set (`DySN`)
`polymer as string`	the polymer (`GTyp`)
`sizeStandard as string`	the size standard of a fragment run (`StdF`)
`runStart as string`	`YYYY-MM-DD HH:MM:SS` from `RUND` / `RUNT` 1
`runFinish as string`	from `RUND` / `RUNT` 2
`collectionStart as string`	from `RUND` / `RUNT` 3
`collectionFinish as string`	from `RUND` / `RUNT` 4

#abif cheatsheet

#Constants

#Files and the directory

#Values

#The run

#Types

#File

#Entry

#Value

#Date

#Time

#Thumb

#Dye

#Calls

#Info