/* gfClientLib - stuff that both blat and pcr clients of
 * genoFind use. */

#ifndef GFCLIENTLIB_H
#define GFCLIENTLIB_H

void gfClientFileArray(char *fileName, char ***retFiles, int *retFileCount);
/* Check if file if .2bit or .nib or .fa.  If so return just that
 * file in a list of one.  Otherwise read all file and treat file
 * as a list of filenames.  */

bioSeq *gfClientSeqList(int fileCount, char *files[], 
	boolean isProt, boolean isTransDna, char *maskType, 
	float minRepDivergence, boolean showStatus);
/* From an array of .fa and .nib file names, create a
 * list of dnaSeqs, which are set up so that upper case is masked and lower case
 * is unmasked sequence. (This is the opposite of the input, but set so that
 * we can use lower case as our primary DNA sequence, which historically predates
 * our use of lower case masking.)  Protein sequence on the other hand is
 * all upper case. */

void gfClientUnmask(struct dnaSeq *seqList);
/* Unmask all sequences. */

#endif /* GFCLIENTLIB_H */