Slice Tools
libSlice
Slice.h File Reference
Detailed Description
Defines interface for libSlice.Library of functions for determining quality values and classes on slices. Include this file to use all publically available methods and data structures.
Definition in file Slice.h.
Go to the source code of this file.
Data Structures | |
| struct | libSlice_BaseDistribution |
| Holds a table of the distribution of bases. More... | |
| struct | libSlice_Consensus |
| Holds the quality value of the onsensus and each of the 5 components. More... | |
| struct | libSlice_Slice |
| Structure for specifing slice information. More... | |
Slice Consensus Calculations | |
| Functions for calculating the consensus and qv of a single slice | |
| void | libSlice_setRecallEmpty (int recallEmpty) |
| Toggles if empty slices should be recalled as gap. | |
| int | libSlice_getConsensusParam (const libSlice_Slice *s, libSlice_Consensus *result, const libSlice_BaseDistribution *dist, int highQualityThreshold, int doAmbiguity) |
| Calculates the consensus quality value for a single slice. | |
| int | libSlice_updateAmbiguityConic (const libSlice_Slice *s, libSlice_Consensus *consensus, int highQuality) |
| Updates the ambiguity flags using the conic model and scoring matrix. | |
| int | libSlice_updateAmbiguity (const libSlice_Slice *s, libSlice_Consensus *consensus, int highQualityThreshold) |
| Updates the ambiguity flags to include all high quality reads. | |
| int | libSlice_getConsensus (const libSlice_Slice *s, libSlice_Consensus *results, const libSlice_BaseDistribution *dist, int highQualityThreshold) |
| Calculates the consensus of a slice with NO ambiguity codes. | |
| int | libSlice_getConsensusWithAmbiguity (const libSlice_Slice *s, libSlice_Consensus *results, const libSlice_BaseDistribution *dist, int highQualityThreshold) |
| Calculates the consensus of a slice with ambiguity codes. | |
SliceRange Consensus Calculations | |
| Functions for calculating the consensus and qv of a range of slices | |
| int | libSlice_getConsensusRangeParam (const libSlice_Slice s[], libSlice_Consensus results[], int len, const libSlice_BaseDistribution *dist, int highQualityThreshold, int doAmbiguity) |
| Calculates the Consensus Quality Values for a range of slices. | |
| int | libSlice_getConsensusRange (const libSlice_Slice s[], libSlice_Consensus results[], int len, const libSlice_BaseDistribution *dist, int highQualityThreshold) |
| Calculates the consensus of an array of slice with no ambiguity codes. | |
| int | libSlice_getConsensusRangeWithAmbiguity (const libSlice_Slice s[], libSlice_Consensus results[], int len, const libSlice_BaseDistribution *dist, int highQualityThreshold) |
| Calculates the consensus of an array of slice with ambiguity codes. | |
Quality Class Calculations | |
| Functions for calculating the quality class of slices | |
| char | libSlice_getConsQC (const libSlice_Slice *s, int highQualityThreshold) |
| Calculates the quality class for a single slice. | |
| char * | libSlice_getConsQCRange (const libSlice_Slice s[], int len, int highQualityThreshold) |
| Calculates the quality classes for a range of slices. | |
Ambiguity Code Calculations | |
| Functions for calculating ambiguity Codes | |
| char | libSlice_getAmbiguityCode (long double cpA, long double cpC, long double cpG, long double cpT, long double cpGap, int highQualityThreshold, int baseCount) |
| Return IUPAC Ambiguity Code in one operation. | |
| char | libSlice_calculateAmbiguityFlags (long double cpA, long double cpC, long double cpG, long double cpT, long double cpGap, int highQualityThreshold, int baseCount) |
| Calculates ambiguity flags from Churchill and Waterman procedure. | |
| char | libSlice_convertAmbiguityFlags (char ambiguityFlags) |
| Calculates extended ambiguity code bases from ambiguity flags. | |
Utility Functions | |
| Other useful functions | |
| char | libSlice_getCompliment (char base) |
| Get the compliment to a base or ambiguity code. | |
| const char * | libSlice_getVersion () |
| Gets a string representing the version of the library. | |
| void * | libSlice_newmem (int number, int size) |
| Error Checking malloc. | |
Defines | |
| #define | HIGH_QUALITY_THRESHOLD 30 |
| What is considered high quality by ABI. | |
| #define | MIN_QUALITY_VALUE 1 |
| Minimum allowed quality value (gap or otherwise). | |
| #define | GAP_QUALITY_VALUE_EMPTY_SLICE 1 |
| Quality value to assign to gap in an empty slice. | |
| #define | MAX_QUALITY_VALUE 4000 |
| Quality Value to return when floating point underflows occur. | |
| #define | AMBIGUITY_FLAGBIT_A 0x1 |
| Bit flag for 'A' in ambiguity code. | |
| #define | AMBIGUITY_FLAGBIT_C 0x2 |
| Bit flag for 'C' in ambiguity code. | |
| #define | AMBIGUITY_FLAGBIT_G 0x4 |
| Bit flag for 'G' in ambiguity code. | |
| #define | AMBIGUITY_FLAGBIT_T 0x8 |
| Bit flag for 'T' in ambiguity code. | |
| #define | AMBIGUITY_FLAGBIT_GAP 0x10 |
| Bit flag for '-' in ambiguity code. | |