e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/genomeRangeTreeFile.h src/hg/inc/genomeRangeTreeFile.h index 5deb03e..4f6473a 100644 --- src/hg/inc/genomeRangeTreeFile.h +++ src/hg/inc/genomeRangeTreeFile.h @@ -1,144 +1,147 @@ /* genomeRangeTreeFile - This module is a way of serializing * and saving genomeRangeTrees, and for modifying saved range trees * by creating a file representing the intersection or union of two * saved genomeRangeTrees. * Also see genomeRangeTree and rangeTree for more information. */ +/* Copyright (C) 2008 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef GENOMERANGETREEFILE_H #define GENOMERANGETREEFILE_H //#ifndef RANGETREE_H //#include "rangeTree.h" //#endif #ifndef GENOMERANGETREE_H #include "genomeRangeTree.h" #endif struct genomeRangeTreeFile /* A structure which stores header, index, and file state information * for a genomeRangeTree saved to a file. */ { struct genomeRangeTreeFile *next; char *name; FILE *file; struct genomeRangeTree *tree; bits32 sig; bits32 version; bits32 headerLen; bits32 numChroms; bits32 valDataSize; bits32 valDataType; bits32 reserved1; bits32 reserved2; boolean isSwapped; struct hashEl *chromList; /* Ordered list of (chrom,rangeTree) hashEls */ struct hash *nodes; /* hash of (chrom, nodes) */ struct hash *offset; /* hash of (chrom, offset) */ }; struct genomeRangeTree *genomeRangeTreeRead(char *fileName); /* Read in the genomeRangeTree data for each chromosome and * return the genomeRangeTree. * Squawk and die if there is a problem. */ void genomeRangeTreeWrite(struct genomeRangeTree *tree, char *fileName); /* Write out genomeRangeTree including: * header portion * index of chromosomes * data for each range tree */ struct genomeRangeTreeFile *genomeRangeTreeFileNew(struct genomeRangeTree *tree, char *fileName); /* Create a genomeRangeTreeFile to save a genomeRangeTree in 'fileName'. * Opens the file. * Call genomeRangeTreeFileWriteHeader() to write the header data only. * Call genomeRangeTreeFileWriteData() to write the data portion only. */ struct genomeRangeTreeFile *genomeRangeTreeFileReadHeader(char *fileName); /* Creates a genomeRangeTreeFile to read a genomeRangeTree from 'fileName'. * Opens the file, reads in header and index. * Leaves file handle open at begining of data portion. * Returns a genomeRangeTreeFile containing file handle and index into contents. * To read genomeRangeTree data use: genomeRangeTreeFileReadData(). * To return genomeRangeTree and close file and index use: genomeRangeTreeFileFree() * Squawk and die if there is a problem. */ struct genomeRangeTree *genomeRangeTreeFileReadData(struct genomeRangeTreeFile *f); /* Read in the genomeRangeTree data for each chromosome and * return the genomeRangeTree. * File handle is left open pointing at the end of the file. * To close and free the genomeRangeTreeFile use: genomeRangeTreeFileFree(). * Squawk and die if there is a problem. */ void genomeRangeTreeFileWriteHeader(struct genomeRangeTreeFile *f); /* Write out genomeRangeTree header including: * header portion * index of chromosomes. * To close the file use: genomeRangeTreeFileFree(). */ void genomeRangeTreeFileWriteData(struct genomeRangeTreeFile *f); /* Write out genomeRangeTree data for each chromosome in chroms. */ struct genomeRangeTree *genomeRangeTreeFileFree(struct genomeRangeTreeFile **pFile); /* Free up the resources associated with a genomeRangeTreeFile. * Close the file. * Return the genomeRangeTree. */ void genomeRangeTreeFileUnionDetailed(struct genomeRangeTreeFile *tf1, struct genomeRangeTreeFile *tf2, char *outFile, int *numChroms, int *nodes, unsigned *size, boolean saveMem, boolean orDirectToFile); /* Create union of two saved genomeRangeTrees through a linear file scan. * Writes resulting genomeRangeTree to outFile. * The resulting file cannot be safely read until the operation is complete. The header * information at the beginning of the file has to be updated after all the data is written * since the number of nodes in the final merged rangeTree is not known until the ranges are merged. * To enforce this, the header is written with a zero initial 'sig' field so that it cannot * be read as a genomeRangeTree file. The header information and 'sig' is re-written with * correct data at the end of the process via an 'fseek' operation to the beginning of the file. * If outFile is null, does not output the file. * The number of nodes in the resulting tree is returned in n. * If size is not NULL, this will return the total size of the resulting ranges (adds 'n' * calculations to run time of program). */ void genomeRangeTreeFileUnion(struct genomeRangeTreeFile *tf1, struct genomeRangeTreeFile *tf2, char *outFile); /* Combine two saved genomeRangeTrees in a logical 'or' through a linear file scan. * Writes resulting genomeRangeTree to outFile. * The resulting file cannot be safely read until the operation is complete. The header * information at the beginning of the file has to be updated after all the data is written * since the final merged rangeTree sizes are not known until the ranges are merged. * To enforce this, the header is written with a zero initial 'sig' field so that it cannot * be read as a genomeRangeTree file. The header information and 'sig' is re-written with * correct data at the end of the process via an 'fseek' operation to the beginning of the file. * If outFile is null, does not output the file. */ void genomeRangeTreeFileIntersectionDetailed(struct genomeRangeTreeFile *tf1, struct genomeRangeTreeFile *tf2, char *outFile, int *numChroms, int *nodes, unsigned *size, boolean saveMem); /* Create intersection genomeRangeTree from two saved genomeRangeTrees in a logical 'and' through a linear file scan. * Writes resulting genomeRangeTree to outFile if outFile is non-null. * Returns number of nodes in n. * Returns total size of ranges if size is non-null. * The resulting file cannot be safely read until the operation is complete. The header * information at the beginning of the file has to be updated after all the data is written * since the final merged rangeTree sizes are not known until the ranges are merged. * To enforce this, the header is written with a zero initial 'sig' field so that it cannot * be read as a genomeRangeTree file. The header information and 'sig' is re-written with * correct data at the end of the process via an 'fseek' operation to the beginning of the file. */ void genomeRangeTreeFileStats(char *fileName, int *numChroms, int *nodes, int *size); /* Calculates the number of chroms, ranges, and total size of ranges in the genomeRangeTree file. * Performs a linear scan of the file. */ int genomeRangeTreeFileChromSeek(struct genomeRangeTreeFile *tf, char *chrom); /* Seek the tree file to the start of the chromosome data. * Returns the number of nodes in the chromosome. * If this chromosome is not in this tree, does not do a seek * and returns 0 for number of nodes. */ void genomeRangeTreeFileWriteToBed(char *inBama, char *bedFile, boolean withId, boolean mergeAdjacent); /* Write a genomeRangeTreeFile directly to a bed file. * If withId then unique identifier is added to the name field. * If mergeAdjacent then adjacent ranges, which would otherwise appear on individual lines, * are merged into a * single bed line. */ #endif /* GENOMERANGETREEFILE_H */