works

[samtools.git] / faidx.h

diff --git a/faidx.h b/faidx.h
index 98c60e4cf1dfbc69e9d6014d96174ca2adaca2e8..1fb1b1fcfab22385f3463c2138fcf1bf6533fef8 100644 (file)
--- a/faidx.h
+++ b/faidx.h
@@ -46,9 +46,10 @@ extern "C" {
        /*!
          @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.
         */
-       void fai_build(const char *fn);
+       int fai_build(const char *fn);
 
        /*!
          @abstract    Distroy a faidx_t struct.
@@ -74,6 +75,27 @@ extern "C" {
         */
        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