git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SICtools@109238 bc3139a8-67e5-0310-9ffc-ced21a209358
James Hester authored on 06/10/2015 17:15:15
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+#ifndef BAM_SAM_H |
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+#define BAM_SAM_H |
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+ |
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+#include "bam.h" |
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+ |
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+/*! |
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+ @header |
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+ |
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+ This file provides higher level of I/O routines and unifies the APIs |
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+ for SAM and BAM formats. These APIs are more convenient and |
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+ recommended. |
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+ |
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+ @copyright Genome Research Ltd. |
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+ */ |
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+ |
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+/*! @typedef |
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+ @abstract SAM/BAM file handler |
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+ @field type type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format |
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+ @field bam BAM file handler; valid if (type&1) == 1 |
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+ @field tamr SAM file handler for reading; valid if type == 2 |
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+ @field tamw SAM file handler for writing; valid if type == 0 |
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+ @field header header struct |
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+ */ |
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+typedef struct {
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+ int type; |
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+ union {
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+ tamFile tamr; |
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+ bamFile bam; |
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+ FILE *tamw; |
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+ } x; |
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+ bam_header_t *header; |
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+} samfile_t; |
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+ |
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+#ifdef __cplusplus |
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+extern "C" {
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+#endif |
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+ |
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+ /*! |
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+ @abstract Open a SAM/BAM file |
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+ |
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+ @param fn SAM/BAM file name; "-" is recognized as stdin (for |
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+ reading) or stdout (for writing). |
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+ |
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+ @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading, |
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+ 'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output, |
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+ 'h' for outputing header in SAM, 'x' for HEX flag and 'X' for |
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+ string flag. If 'b' present, it must immediately follow 'r' or |
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+ 'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX", |
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+ "rb", "wb" and "wbu" exclusively. |
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+ |
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+ @param aux auxiliary data; if mode[0]=='w', aux points to |
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+ bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM |
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+ are absent, aux points the file name of the list of the reference; |
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+ aux is not used otherwise. If @SQ header lines are present in SAM, |
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+ aux is not used, either. |
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+ |
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+ @return SAM/BAM file handler |
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+ */ |
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+ samfile_t *samopen(const char *fn, const char *mode, const void *aux); |
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+ |
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+ /*! |
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+ @abstract Close a SAM/BAM handler |
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+ @param fp file handler to be closed |
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+ */ |
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+ void samclose(samfile_t *fp); |
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+ |
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+ /*! |
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+ @abstract Read one alignment |
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+ @param fp file handler |
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+ @param b alignment |
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+ @return bytes read |
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+ */ |
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+ int samread(samfile_t *fp, bam1_t *b); |
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+ |
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+ /*! |
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+ @abstract Write one alignment |
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+ @param fp file handler |
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+ @param b alignment |
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+ @return bytes written |
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+ */ |
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+ int samwrite(samfile_t *fp, const bam1_t *b); |
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+ |
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+ /*! |
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+ @abstract Get the pileup for a whole alignment file |
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+ @param fp file handler |
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+ @param mask mask transferred to bam_plbuf_set_mask() |
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+ @param func user defined function called in the pileup process |
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+ #param data user provided data for func() |
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+ */ |
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+ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data); |
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+ |
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+ char *samfaipath(const char *fn_ref); |
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+ int samthreads(samfile_t *fp, int n_threads, int n_sub_blks); |
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+ |
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+#ifdef __cplusplus |
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+} |
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+#endif |
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+ |
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+#endif |