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author | ryanmorin |
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date | Tue, 18 Oct 2011 18:33:15 -0400 |
parents | 74f5ea818cea |
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#ifndef BAM_SAM_H #define BAM_SAM_H #include "bam.h" /*! @header This file provides higher level of I/O routines and unifies the APIs for SAM and BAM formats. These APIs are more convenient and recommended. @copyright Genome Research Ltd. */ /*! @typedef @abstract SAM/BAM file handler @field type type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format @field bam BAM file handler; valid if (type&1) == 1 @field tamr SAM file handler for reading; valid if type == 2 @field tamw SAM file handler for writing; valid if type == 0 @field header header struct */ typedef struct { int type; union { tamFile tamr; bamFile bam; FILE *tamw; } x; bam_header_t *header; } samfile_t; #ifdef __cplusplus extern "C" { #endif /*! @abstract Open a SAM/BAM file @param fn SAM/BAM file name; "-" is recognized as stdin (for reading) or stdout (for writing). @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading, 'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output, 'h' for outputing header in SAM, 'x' for HEX flag and 'X' for string flag. If 'b' present, it must immediately follow 'r' or 'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX", "rb", "wb" and "wbu" exclusively. @param aux auxiliary data; if mode[0]=='w', aux points to bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM are absent, aux points the file name of the list of the reference; aux is not used otherwise. If @SQ header lines are present in SAM, aux is not used, either. @return SAM/BAM file handler */ samfile_t *samopen(const char *fn, const char *mode, const void *aux); /*! @abstract Close a SAM/BAM handler @param fp file handler to be closed */ void samclose(samfile_t *fp); /*! @abstract Read one alignment @param fp file handler @param b alignment @return bytes read */ int samread(samfile_t *fp, bam1_t *b); /*! @abstract Write one alignment @param fp file handler @param b alignment @return bytes written */ int samwrite(samfile_t *fp, const bam1_t *b); /*! @abstract Get the pileup for a whole alignment file @param fp file handler @param mask mask transferred to bam_plbuf_set_mask() @param func user defined function called in the pileup process #param data user provided data for func() */ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data); char *samfaipath(const char *fn_ref); #ifdef __cplusplus } #endif #endif