ajassem.c

Datatypes:

AjPAssem Assembly data

AjPAssemRead Assembly read data

AjPAssemReadgroup Assembly read group data

AjEAssemPlatform Assembly platform

AjEAssemSortOrder Assembly sort order

none Miscellaneous functions

Datatype: AjPAssem

Function is for manipulating assembly data objects

Sections:

constructors Constructors

Assem data destructors Destructors

Casts Casts

assembly data modifiers Modifiers

AjPAssem: constructors

Constructors

Functions:

ajAssemNew Assem data constructor

Function ajAssemNew

Assem data constructor

Prototype

AjPAssem ajAssemNew (
      void
);

Type Name Read/Write Description

AjPAssem RETURN New object

Type	Name	Read/Write	Description
`AjPAssem`		RETURN	New object

From EMBOSS 6.4.0

AjPAssem: Assem data destructors

Destruction destroys all internal data structures and frees the memory allocated for the assembly data object.

Functions:

ajAssemDel Assem data destructor

Function ajAssemDel

Assem data destructor

Prototype

void ajAssemDel (
      AjPAssem* Passem
);

Type Name Read/Write Description

AjPAssem* Passem Delete Assem data object to delete

void RETURN

Type	Name	Read/Write	Description
`AjPAssem*`	`Passem`	Delete	Assem data object to delete
`void`		RETURN

From EMBOSS 6.4.0

AjPAssem: Casts

Return values from an assembly data object

Functions:

ajAssemGetId Return the identifier

ajAssemGetQryC Returns the query string of an assembly data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

ajAssemGetQryS Returns the query string of an assembly data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

ajAssemGetSortorderC Returns sort-order name of the given assembly

Function ajAssemGetId

Return the identifier

Prototype

const AjPStr ajAssemGetId (
      const AjPAssem assem
);

Type Name Read/Write Description

const AjPAssem assem Input Assembly

const AjPStr RETURN Returned id

Type	Name	Read/Write	Description
`const AjPAssem`	`assem`	Input	Assembly
`const AjPStr`		RETURN	Returned id

From EMBOSS 6.5.0

Function ajAssemGetQryC

Returns the query string of an assembly data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajAssemGetQryC (
      const AjPAssem assem
);

Type Name Read/Write Description

const AjPAssem assem Input Assem data object.

const char* RETURN Query as a character string.

Type	Name	Read/Write	Description
`const AjPAssem`	`assem`	Input	Assem data object.
`const char*`		RETURN	Query as a character string.

From EMBOSS 6.4.0

Function ajAssemGetQryS

Prototype

const AjPStr ajAssemGetQryS (
      const AjPAssem assem
);

Type Name Read/Write Description

const AjPAssem assem Input Assem data object.

const AjPStr RETURN Query as a string.

Type	Name	Read/Write	Description
`const AjPAssem`	`assem`	Input	Assem data object.
`const AjPStr`		RETURN	Query as a string.

From EMBOSS 6.4.0

Function ajAssemGetSortorderC

Returns sort-order name of the given assembly

Prototype

const char* ajAssemGetSortorderC (
      const AjPAssem assem
);

Type Name Read/Write Description

const AjPAssem assem Input assembly

const char* RETURN sort-order name

Type	Name	Read/Write	Description
`const AjPAssem`	`assem`	Input	assembly
`const char*`		RETURN	sort-order name

From EMBOSS 6.5.0

AjPAssem: assembly data modifiers

Assem data modifiers

Functions:

ajAssemClear Resets all data for an assembly data object so that it can be reused.

ajAssemReset Resets read data for an assembly data object so that it can be reused.

ajAssemSetContigattributes Set contig attributes uri, md5, species and assemblyid using the values provided in contigtags table.

ajAssemSetReadgroups Set assembly readgroups using the values in readgrouptags table

Function ajAssemClear

Resets all data for an assembly data object so that it can be reused.

Prototype

void ajAssemClear (
      AjPAssem assem
);

Type Name Read/Write Description

AjPAssem assem Modify assem data

void RETURN

Type	Name	Read/Write	Description
`AjPAssem`	`assem`	Modify	assem data
`void`		RETURN

From EMBOSS 6.4.0

Function ajAssemReset

Resets read data for an assembly data object so that it can be reused.

Prototype

void ajAssemReset (
      AjPAssem assem
);

Type Name Read/Write Description

AjPAssem assem Modify assem data

void RETURN

Type	Name	Read/Write	Description
`AjPAssem`	`assem`	Modify	assem data
`void`		RETURN

From EMBOSS 6.5.0

Function ajAssemSetContigattributes

Set contig attributes uri, md5, species and assemblyid using the values provided in contigtags table.

Prototype

void ajAssemSetContigattributes (
      AjPAssem assem,
      const AjPTable tags
);

Type Name Read/Write Description

AjPAssem assem Modify Assembly object

const AjPTable tags Input Table of tables for contig tags. Main table have an entry for each contig. Sub-tables include tag values for a contig.

void RETURN

Type	Name	Read/Write	Description
`AjPAssem`	`assem`	Modify	Assembly object
`const AjPTable`	`tags`	Input	Table of tables for contig tags. Main table have an entry for each contig. Sub-tables include tag values for a contig.
`void`		RETURN

From EMBOSS 6.5.0

Function ajAssemSetReadgroups

Set assembly readgroups using the values in readgrouptags table

Prototype

void ajAssemSetReadgroups (
      AjPAssem assem,
      const AjPTable tags
);

Type Name Read/Write Description

AjPAssem assem Modify Assembly object

const AjPTable tags Input Table of tables for readgroup tags. Main table have an entry for each read-group. Sub-tables include tag values for a read-group.

void RETURN

Type	Name	Read/Write	Description
`AjPAssem`	`assem`	Modify	Assembly object
`const AjPTable`	`tags`	Input	Table of tables for readgroup tags. Main table have an entry for each read-group. Sub-tables include tag values for a read-group.
`void`		RETURN

From EMBOSS 6.5.0

Datatype: AjPAssemRead

Function is for manipulating assembly read objects

Sections:

Assembly read data destructors Destructors

Casts Casts

assembly read data modifiers Modifiers

AjPAssemRead: Assembly read data destructors

Destruction destroys all internal data structures and frees the memory allocated for the assembly read data object.

Functions:

ajAssemreadDel Delete assembly read/alignment records

Function ajAssemreadDel

Delete assembly read/alignment records

Prototype

void ajAssemreadDel (
      AjPAssemRead* Passemread
);

Type Name Read/Write Description

AjPAssemRead* Passemread Delete Assembly read object to delete

void RETURN

Type	Name	Read/Write	Description
`AjPAssemRead*`	`Passemread`	Delete	Assembly read object to delete
`void`		RETURN

From EMBOSS 6.5.0

AjPAssemRead: Casts

Return values from an assembly read data object

Functions:

ajAssemreadGetAlignmentend 1-based inclusive rightmost position of the clipped sequence, or 0 if read unmapped

ajAssemreadGetAlignmentstart Return alignment start (1-based)

ajAssemreadGetFlagFirstofpair Return whether the read is the first read in a pair

ajAssemreadGetFlagNegativestrand Return strand of the query (false for forward; true for reverse strand)

ajAssemreadGetFlagPaired Return whether the read is paired in sequencing, no matter whether it is mapped in a pair

ajAssemreadGetFlagUnmapped Return whether the read is unmapped

Function ajAssemreadGetAlignmentend

1-based inclusive rightmost position of the clipped sequence, or 0 if read unmapped

Prototype

ajint ajAssemreadGetAlignmentend (
      const AjPAssemRead r
);

Type Name Read/Write Description

const AjPAssemRead r Input read

ajint RETURN end position of the alignment on the reference sequence

Type	Name	Read/Write	Description
`const AjPAssemRead`	`r`	Input	read
`ajint`		RETURN	end position of the alignment on the reference sequence

From EMBOSS 6.5.0

Function ajAssemreadGetAlignmentstart

Return alignment start (1-based)

Prototype

ajint ajAssemreadGetAlignmentstart (
      const AjPAssemRead r
);

Type Name Read/Write Description

const AjPAssemRead r Input read

ajint RETURN start position of the alignment on the reference sequence

Type	Name	Read/Write	Description
`const AjPAssemRead`	`r`	Input	read
`ajint`		RETURN	start position of the alignment on the reference sequence

From EMBOSS 6.5.0

Function ajAssemreadGetFlagFirstofpair

Return whether the read is the first read in a pair

Prototype

AjBool ajAssemreadGetFlagFirstofpair (
      const AjPAssemRead r
);

Type Name Read/Write Description

const AjPAssemRead r Input read

AjBool RETURN true if the read is the first read in a pair

Type	Name	Read/Write	Description
`const AjPAssemRead`	`r`	Input	read
`AjBool`		RETURN	true if the read is the first read in a pair

From EMBOSS 6.5.0

Function ajAssemreadGetFlagNegativestrand

Return strand of the query (false for forward; true for reverse strand)

Prototype

AjBool ajAssemreadGetFlagNegativestrand (
      const AjPAssemRead r
);

Type Name Read/Write Description

const AjPAssemRead r Input read

AjBool RETURN true if the read is reverse strand

Type	Name	Read/Write	Description
`const AjPAssemRead`	`r`	Input	read
`AjBool`		RETURN	true if the read is reverse strand

From EMBOSS 6.5.0

Function ajAssemreadGetFlagPaired

Return whether the read is paired in sequencing, no matter whether it is mapped in a pair

Prototype

AjBool ajAssemreadGetFlagPaired (
      const AjPAssemRead r
);

Type Name Read/Write Description

const AjPAssemRead r Input read

AjBool RETURN true if the read is paired

Type	Name	Read/Write	Description
`const AjPAssemRead`	`r`	Input	read
`AjBool`		RETURN	true if the read is paired

From EMBOSS 6.5.0

Function ajAssemreadGetFlagUnmapped

Return whether the read is unmapped

Prototype

AjBool ajAssemreadGetFlagUnmapped (
      const AjPAssemRead r
);

Type Name Read/Write Description

const AjPAssemRead r Input read

AjBool RETURN true if the read is unmapped

Type	Name	Read/Write	Description
`const AjPAssemRead`	`r`	Input	read
`AjBool`		RETURN	true if the read is unmapped

From EMBOSS 6.5.0

AjPAssemRead: assembly read data modifiers

Assem data modifiers

Functions:

ajAssemreadSetAlignblocks Returns blocks of the read sequence that have been aligned directly to the reference sequence. Clipped portions of the read and inserted and deleted bases (vs. the reference) are not represented in the alignment blocks.

Function ajAssemreadSetAlignblocks

Returns blocks of the read sequence that have been aligned directly to the reference sequence. Clipped portions of the read and inserted and deleted bases (vs. the reference) are not represented in the alignment blocks.

Prototype

AjPList ajAssemreadSetAlignblocks (
      AjPAssemRead r
);

Type Name Read/Write Description

AjPAssemRead r Modify read/alignment 8

AjPList RETURN list of alignment blocks

Type	Name	Read/Write	Description
`AjPAssemRead`	`r`	Modify	read/alignment 8
`AjPList`		RETURN	list of alignment blocks

From EMBOSS 6.5.0

Datatype: AjPAssemReadgroup

Function is for manipulating assembly data objects

Sections:

Assembly read group functions Miscellaneous

AjPAssemReadgroup: Assembly read group functions

Function is for manipulating read group data

Functions:

ajAssemreadgroupGetPlatformname Returns platform name of the given read-group

Function ajAssemreadgroupGetPlatformname

Returns platform name of the given read-group

Prototype

const char* ajAssemreadgroupGetPlatformname (
      const AjPAssemReadgroup rg
);

Type Name Read/Write Description

const AjPAssemReadgroup rg Input read group

const char* RETURN platform name

Type	Name	Read/Write	Description
`const AjPAssemReadgroup`	`rg`	Input	read group
`const char*`		RETURN	platform name

From EMBOSS 6.5.0

Datatype: AjEAssemPlatform

Function is for manipulating assembly platform enumerations

Sections:

Assembly platform functions Miscellaneous

AjEAssemPlatform: Assembly platform functions

Function is for manipulating assembly platform enumerations

Functions:

ajAssemplatformGetType Returns platform type enumeration for the given platform

Function ajAssemplatformGetType

Returns platform type enumeration for the given platform

Prototype

AjEAssemPlatform ajAssemplatformGetType (
      const char* name
);

Type Name Read/Write Description

const char* name Input platform name

AjEAssemPlatform RETURN platform type

Type	Name	Read/Write	Description
`const char*`	`name`	Input	platform name
`AjEAssemPlatform`		RETURN	platform type

From EMBOSS 6.5.0

Datatype: AjEAssemSortOrder

Function is for manipulating assembly sort order enumerations

Sections:

Assembly sort order functions Miscellaneous

AjEAssemSortOrder: Assembly sort order functions

Function is for manipulating assembly sort-order enumerations

Functions:

ajAssemsortorderGetType Returns sort-order type for the given sort-order-name

Function ajAssemsortorderGetType

Returns sort-order type for the given sort-order-name

Prototype

AjEAssemSortOrder ajAssemsortorderGetType (
      const char* name
);

Type Name Read/Write Description

const char* name Input sort order name

AjEAssemSortOrder RETURN sort order type

Type	Name	Read/Write	Description
`const char*`	`name`	Input	sort order name
`AjEAssemSortOrder`		RETURN	sort order type

From EMBOSS 6.5.0

Prototype

void ajAssemExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.4.0

AjPAssem	Assembly data
AjPAssemRead	Assembly read data
AjPAssemReadgroup	Assembly read group data
AjEAssemPlatform	Assembly platform
AjEAssemSortOrder	Assembly sort order
none	Miscellaneous functions

constructors	Constructors
Assem data destructors	Destructors
Casts	Casts
assembly data modifiers	Modifiers

ajAssemGetId	Return the identifier
ajAssemGetQryC	Returns the query string of an assembly data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajAssemGetQryS	Returns the query string of an assembly data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajAssemGetSortorderC	Returns sort-order name of the given assembly

ajAssemClear	Resets all data for an assembly data object so that it can be reused.
ajAssemReset	Resets read data for an assembly data object so that it can be reused.
ajAssemSetContigattributes	Set contig attributes uri, md5, species and assemblyid using the values provided in contigtags table.
ajAssemSetReadgroups	Set assembly readgroups using the values in readgrouptags table

Assembly read data destructors	Destructors
Casts	Casts
assembly read data modifiers	Modifiers

ajAssemreadGetAlignmentend	1-based inclusive rightmost position of the clipped sequence, or 0 if read unmapped
ajAssemreadGetAlignmentstart	Return alignment start (1-based)
ajAssemreadGetFlagFirstofpair	Return whether the read is the first read in a pair
ajAssemreadGetFlagNegativestrand	Return strand of the query (false for forward; true for reverse strand)
ajAssemreadGetFlagPaired	Return whether the read is paired in sequencing, no matter whether it is mapped in a pair
ajAssemreadGetFlagUnmapped	Return whether the read is unmapped