diff PsiCLASS-1.0.2/samtools-0.1.19/faidx.h @ 0:903fc43d6227 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/faidx.h	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,103 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <[e-mail]> */
+
+#ifndef FAIDX_H
+#define FAIDX_H
+
+/*!
+  @header
+
+  Index FASTA files and extract subsequence.
+
+  @copyright The Wellcome Trust Sanger Institute.
+ */
+
+struct __faidx_t;
+typedef struct __faidx_t faidx_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	/*!
+	  @abstract   Build index for a FASTA or razip compressed FASTA file.
+	  @param  fn  FASTA file name
+	  @return     0 on success; or -1 on failure
+	  @discussion File "fn.fai" will be generated.
+	 */
+	int fai_build(const char *fn);
+
+	/*!
+	  @abstract    Distroy a faidx_t struct.
+	  @param  fai  Pointer to the struct to be destroyed
+	 */
+	void fai_destroy(faidx_t *fai);
+
+	/*!
+	  @abstract   Load index from "fn.fai".
+	  @param  fn  File name of the FASTA file
+	 */
+	faidx_t *fai_load(const char *fn);
+
+	/*!
+	  @abstract    Fetch the sequence in a region.
+	  @param  fai  Pointer to the faidx_t struct
+	  @param  reg  Region in the format "chr2:20,000-30,000"
+	  @param  len  Length of the region
+	  @return      Pointer to the sequence; null on failure
+
+	  @discussion The returned sequence is allocated by malloc family
+	  and should be destroyed by end users by calling free() on it.
+	 */
+	char *fai_fetch(const faidx_t *fai, const char *reg, int *len);
+
+	/*!
+	  @abstract	   Fetch the number of sequences. 
+	  @param  fai  Pointer to the faidx_t struct
+	  @return	   The number of sequences
+	 */
+	int faidx_fetch_nseq(const faidx_t *fai);
+
+	/*!
+	  @abstract    Fetch the sequence in a region.
+	  @param  fai  Pointer to the faidx_t struct
+	  @param  c_name Region name
+	  @param  p_beg_i  Beginning position number (zero-based)
+	  @param  p_end_i  End position number (zero-based)
+	  @param  len  Length of the region
+	  @return      Pointer to the sequence; null on failure
+
+	  @discussion The returned sequence is allocated by malloc family
+	  and should be destroyed by end users by calling free() on it.
+	 */
+	char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif