* Re: ffi-help: status to 19 Aug 2017
2017-11-10 1:00 ` Matt Wette
@ 2017-11-10 2:34 ` Matt Wette
0 siblings, 0 replies; 14+ messages in thread
From: Matt Wette @ 2017-11-10 2:34 UTC (permalink / raw)
To: Roel Janssen; +Cc: Guile User, guile-devel
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> On Nov 9, 2017, at 5:00 PM, Matt Wette <matt.wette@gmail.com> wrote:
>
>> On Nov 9, 2017, at 11:10 AM, Roel Janssen <roel@gnu.org> wrote:
>>> ...
>>
>> Thanks for creating this! It seems to be very useful and powerful.
>>
>> I wanted to try ffi-helper on htslib, but I am confused on how to get
>> started. Where does the "compile-ffi" subcommand for "guild" come from?
>>
>> Kind regards,
>> Roel Janssen
>
> See the following, but I'm seeing a parse error so may be a bug in my C99 parser. And not sure "hts.h" is the only include you need.
I got it to compile-ffi. Still a few warnings I need to chase down.
I made a couple fixes (and added examples/ffi/htslib.ffi) and pushed to my repo on savannah.
Also, htslib.scm is attached. It is 1700 lines only.
Matt
[-- Attachment #2: htslib.scm --]
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;; generated with `guild compile-ffi ffi/htslib.ffi'
(define-module (ffi htslib)
#:use-module (system ffi-help-rt)
#:use-module ((system foreign) #:prefix ffi:)
#:use-module (bytestructures guile)
)
(define link-lib (dynamic-link "libhts"))
;; enum htsLogLevel {
;; HTS_LOG_OFF,
;; HTS_LOG_ERROR,
;; HTS_LOG_WARNING = 3,
;; HTS_LOG_INFO,
;; HTS_LOG_DEBUG,
;; HTS_LOG_TRACE,
;; };
(define enum-htsLogLevel-enum-nvl
'((HTS_LOG_OFF . 0)
(HTS_LOG_ERROR . 1)
(HTS_LOG_WARNING . 3)
(HTS_LOG_INFO . 4)
(HTS_LOG_DEBUG . 5)
(HTS_LOG_TRACE . 6))
)
(define enum-htsLogLevel-enum-vnl
(map (lambda (pair) (cons (cdr pair) (car pair)))
enum-htsLogLevel-enum-nvl))
(define-public (unwrap-enum-htsLogLevel n)
(cond
((symbol? n)
(or (assq-ref enum-htsLogLevel-enum-nvl n) (error "bad arg")))
((integer? n) n)
(else (error "bad arg"))))
(define-public (wrap-enum-htsLogLevel v)
(assq-ref enum-htsLogLevel-enum-vnl v))
;; void hts_set_log_level(enum htsLogLevel level);
(define ~hts_set_log_level
(delay (fh-link-proc
"hts_set_log_level"
ffi:void
(list ffi:int)
link-lib)))
(define (hts_set_log_level level)
(let ((~level (unwrap-enum level)))
((force ~hts_set_log_level) ~level)))
(export hts_set_log_level)
;; enum htsLogLevel hts_get_log_level();
(define ~hts_get_log_level
(delay (fh-link-proc
"hts_get_log_level"
ffi:int
(list)
link-lib)))
(define (hts_get_log_level)
(let () (wrap-enum ((force ~hts_get_log_level)))))
(export hts_get_log_level)
;; extern int hts_verbose;
(define hts_verbose
(let* ((addr #f)
(memoize-addr
(lambda ()
(unless
addr
(set! addr
(make-bytestructure
(ffi:pointer->bytevector
(dynamic-pointer "hts_verbose" (dynamic-link))
(ffi:sizeof '*))
0
(bs:pointer int)))))))
(case-lambda
(() (memoize-addr) (bytestructure-ref addr '*)))))
(export hts_verbose)
;; void hts_log(enum htsLogLevel severity, const char *context, const char *
;; format, ...);
;; ... failed.
;; typedef struct BGZF BGZF;
(define-public BGZF-desc 'void)
(define-public BGZF*-desc (bs:pointer BGZF-desc))
(define-fh-pointer-type BGZF* BGZF*-desc BGZF*? make-BGZF*)
(export BGZF* BGZF*? make-BGZF*)
;; typedef struct __kstring_t {
;; size_t l, m;
;; char *s;
;; } kstring_t;
;; == kstring_t =>
(define-public kstring_t-desc
(bs:struct
(list `(m ,size_t)
`(l ,size_t)
`(s ,(bs:pointer int8)))))
(define-fh-compound-type kstring_t kstring_t-desc kstring_t? make-kstring_t)
(export kstring_t kstring_t? make-kstring_t)
(define-public kstring_t*-desc
(bs:pointer kstring_t-desc))
(define-fh-pointer-type kstring_t* kstring_t*-desc kstring_t*? make-kstring_t*
)
(export kstring_t* kstring_t*? make-kstring_t*)
(ref<->deref!
kstring_t*
make-kstring_t*
kstring_t
make-kstring_t)
;; == struct-__kstring_t =>
(define-public struct-__kstring_t-desc
kstring_t-desc)
(define-fh-compound-type struct-__kstring_t struct-__kstring_t-desc
struct-__kstring_t? make-struct-__kstring_t)
(export struct-__kstring_t struct-__kstring_t? make-struct-__kstring_t)
(define-public struct-__kstring_t*-desc
kstring_t*-desc)
(define-fh-pointer-type struct-__kstring_t* struct-__kstring_t*-desc
struct-__kstring_t*? make-struct-__kstring_t*)
(export struct-__kstring_t* struct-__kstring_t*? make-struct-__kstring_t*)
(ref<->deref!
struct-__kstring_t*
make-struct-__kstring_t*
struct-__kstring_t
make-struct-__kstring_t)
;; enum htsFormatCategory {
;; unknown_category,
;; sequence_data,
;; variant_data,
;; index_file,
;; region_list,
;; category_maximum = 32767,
;; };
(define enum-htsFormatCategory-enum-nvl
'((unknown_category . 0)
(sequence_data . 1)
(variant_data . 2)
(index_file . 3)
(region_list . 4)
(category_maximum . 32767))
)
(define enum-htsFormatCategory-enum-vnl
(map (lambda (pair) (cons (cdr pair) (car pair)))
enum-htsFormatCategory-enum-nvl))
(define-public (unwrap-enum-htsFormatCategory n)
(cond
((symbol? n)
(or (assq-ref enum-htsFormatCategory-enum-nvl n) (error "bad arg")))
((integer? n) n)
(else (error "bad arg"))))
(define-public (wrap-enum-htsFormatCategory v)
(assq-ref enum-htsFormatCategory-enum-vnl v))
;; enum htsExactFormat {
;; unknown_format,
;; binary_format,
;; text_format,
;; sam,
;; bam,
;; bai,
;; cram,
;; crai,
;; vcf,
;; bcf,
;; csi,
;; gzi,
;; tbi,
;; bed,
;; htsget,
;; json = htsget,
;; format_maximum = 32767,
;; };
(define enum-htsExactFormat-enum-nvl
'((unknown_format . 0)
(binary_format . 1)
(text_format . 2)
(sam . 3)
(bam . 4)
(bai . 5)
(cram . 6)
(crai . 7)
(vcf . 8)
(bcf . 9)
(csi . 10)
(gzi . 11)
(tbi . 12)
(bed . 13)
(htsget . 14)
(json . 14)
(format_maximum . 32767))
)
(define enum-htsExactFormat-enum-vnl
(map (lambda (pair) (cons (cdr pair) (car pair)))
enum-htsExactFormat-enum-nvl))
(define-public (unwrap-enum-htsExactFormat n)
(cond
((symbol? n)
(or (assq-ref enum-htsExactFormat-enum-nvl n) (error "bad arg")))
((integer? n) n)
(else (error "bad arg"))))
(define-public (wrap-enum-htsExactFormat v)
(assq-ref enum-htsExactFormat-enum-vnl v))
;; enum htsCompression {
;; no_compression,
;; gzip,
;; bgzf,
;; custom,
;; compression_maximum = 32767,
;; };
(define enum-htsCompression-enum-nvl
'((no_compression . 0)
(gzip . 1)
(bgzf . 2)
(custom . 3)
(compression_maximum . 32767))
)
(define enum-htsCompression-enum-vnl
(map (lambda (pair) (cons (cdr pair) (car pair)))
enum-htsCompression-enum-nvl))
(define-public (unwrap-enum-htsCompression n)
(cond
((symbol? n)
(or (assq-ref enum-htsCompression-enum-nvl n) (error "bad arg")))
((integer? n) n)
(else (error "bad arg"))))
(define-public (wrap-enum-htsCompression v)
(assq-ref enum-htsCompression-enum-vnl v))
;; typedef struct htsFormat {
;; enum htsFormatCategory category;
;; enum htsExactFormat format;
;; struct {
;; short major, minor;
;; } version;
;; enum htsCompression compression;
;; short compression_level; /* currently unused*/
;; void *specific; /* format specific options; see struct hts_opt.*/
;; } htsFormat;
;; == htsFormat =>
(define-public htsFormat-desc
(bs:struct
(list `(category ,int)
`(format ,int)
`(version
,(bs:struct
(list `(minor ,short) `(major ,short))))
`(compression ,int)
`(compression_level ,short)
`(specific ,(bs:pointer 'void)))))
(define-fh-compound-type htsFormat htsFormat-desc htsFormat? make-htsFormat)
(export htsFormat htsFormat? make-htsFormat)
(define-public htsFormat*-desc
(bs:pointer htsFormat-desc))
(define-fh-pointer-type htsFormat* htsFormat*-desc htsFormat*? make-htsFormat*
)
(export htsFormat* htsFormat*? make-htsFormat*)
(ref<->deref!
htsFormat*
make-htsFormat*
htsFormat
make-htsFormat)
;; == struct-htsFormat =>
(define-public struct-htsFormat-desc
htsFormat-desc)
(define-fh-compound-type struct-htsFormat struct-htsFormat-desc
struct-htsFormat? make-struct-htsFormat)
(export struct-htsFormat struct-htsFormat? make-struct-htsFormat)
(define-public struct-htsFormat*-desc
htsFormat*-desc)
(define-fh-pointer-type struct-htsFormat* struct-htsFormat*-desc
struct-htsFormat*? make-struct-htsFormat*)
(export struct-htsFormat* struct-htsFormat*? make-struct-htsFormat*)
(ref<->deref!
struct-htsFormat*
make-struct-htsFormat*
struct-htsFormat
make-struct-htsFormat)
;; typedef struct {
;; uint32_t is_bin : 1, is_write : 1, is_be : 1, is_cram : 1, is_bgzf : 1,
;; dummy : 27;
;; int64_t lineno;
;; kstring_t line;
;; char *fn, *fn_aux;
;; union {
;; BGZF *bgzf;
;; struct cram_fd *cram;
;; struct hFILE *hfile;
;; } fp;
;; htsFormat format;
;; } htsFile;
(define-public htsFile-desc
(bs:struct
(list `(dummy ,uint64 27)
`(is_bgzf ,uint64 1)
`(is_cram ,uint64 1)
`(is_be ,uint64 1)
`(is_write ,uint64 1)
`(is_bin ,uint64 1)
`(lineno ,int32)
`(line ,kstring_t-desc)
`(fn_aux ,(bs:pointer int8))
`(fn ,(bs:pointer int8))
`(fp ,(bs:union
(list `(bgzf ,BGZF*-desc)
`(cram ,(bs:pointer 'void))
`(hfile ,(bs:pointer 'void)))))
`(format ,htsFormat-desc))))
(define-fh-compound-type htsFile htsFile-desc htsFile? make-htsFile)
(export htsFile htsFile? make-htsFile)
(define-public htsFile*-desc
(bs:pointer htsFile-desc))
(define-fh-pointer-type htsFile* htsFile*-desc htsFile*? make-htsFile*)
(export htsFile* htsFile*? make-htsFile*)
(ref<->deref!
htsFile*
make-htsFile*
htsFile
make-htsFile)
;; typedef struct {
;; struct hts_tpool *pool; /* The shared thread pool itself*/
;; int qsize; /* Size of I/O queue to use for this fp*/
;; } htsThreadPool;
(define-public htsThreadPool-desc
(bs:struct
(list `(pool ,(bs:pointer 'void)) `(qsize ,int))))
(define-fh-compound-type htsThreadPool htsThreadPool-desc htsThreadPool?
make-htsThreadPool)
(export htsThreadPool htsThreadPool? make-htsThreadPool)
(define-public htsThreadPool*-desc
(bs:pointer htsThreadPool-desc))
(define-fh-pointer-type htsThreadPool* htsThreadPool*-desc htsThreadPool*?
make-htsThreadPool*)
(export htsThreadPool* htsThreadPool*? make-htsThreadPool*)
(ref<->deref!
htsThreadPool*
make-htsThreadPool*
htsThreadPool
make-htsThreadPool)
;; enum sam_fields {
;; SAM_QNAME = 0x00000001,
;; SAM_FLAG = 0x00000002,
;; SAM_RNAME = 0x00000004,
;; SAM_POS = 0x00000008,
;; SAM_MAPQ = 0x00000010,
;; SAM_CIGAR = 0x00000020,
;; SAM_RNEXT = 0x00000040,
;; SAM_PNEXT = 0x00000080,
;; SAM_TLEN = 0x00000100,
;; SAM_SEQ = 0x00000200,
;; SAM_QUAL = 0x00000400,
;; SAM_AUX = 0x00000800,
;; SAM_RGAUX = 0x00001000,
;; };
(define enum-sam_fields-enum-nvl
'((SAM_QNAME . 1)
(SAM_FLAG . 2)
(SAM_RNAME . 4)
(SAM_POS . 8)
(SAM_MAPQ . 16)
(SAM_CIGAR . 32)
(SAM_RNEXT . 64)
(SAM_PNEXT . 128)
(SAM_TLEN . 256)
(SAM_SEQ . 512)
(SAM_QUAL . 1024)
(SAM_AUX . 2048)
(SAM_RGAUX . 4096))
)
(define enum-sam_fields-enum-vnl
(map (lambda (pair) (cons (cdr pair) (car pair)))
enum-sam_fields-enum-nvl))
(define-public (unwrap-enum-sam_fields n)
(cond
((symbol? n)
(or (assq-ref enum-sam_fields-enum-nvl n) (error "bad arg")))
((integer? n) n)
(else (error "bad arg"))))
(define-public (wrap-enum-sam_fields v)
(assq-ref enum-sam_fields-enum-vnl v))
;; enum hts_fmt_option {
;; CRAM_OPT_DECODE_MD,
;; CRAM_OPT_PREFIX,
;; CRAM_OPT_VERBOSITY,
;; CRAM_OPT_SEQS_PER_SLICE,
;; CRAM_OPT_SLICES_PER_CONTAINER,
;; CRAM_OPT_RANGE,
;; CRAM_OPT_VERSION,
;; CRAM_OPT_EMBED_REF,
;; CRAM_OPT_IGNORE_MD5,
;; CRAM_OPT_REFERENCE,
;; CRAM_OPT_MULTI_SEQ_PER_SLICE,
;; CRAM_OPT_NO_REF,
;; CRAM_OPT_USE_BZIP2,
;; CRAM_OPT_SHARED_REF,
;; CRAM_OPT_NTHREADS,
;; CRAM_OPT_THREAD_POOL,
;; CRAM_OPT_USE_LZMA,
;; CRAM_OPT_USE_RANS,
;; CRAM_OPT_REQUIRED_FIELDS,
;; CRAM_OPT_LOSSY_NAMES,
;; CRAM_OPT_BASES_PER_SLICE,
;; HTS_OPT_COMPRESSION_LEVEL = 100,
;; HTS_OPT_NTHREADS,
;; HTS_OPT_THREAD_POOL,
;; HTS_OPT_CACHE_SIZE,
;; HTS_OPT_BLOCK_SIZE,
;; };
(define enum-hts_fmt_option-enum-nvl
'((CRAM_OPT_DECODE_MD . 0)
(CRAM_OPT_PREFIX . 1)
(CRAM_OPT_VERBOSITY . 2)
(CRAM_OPT_SEQS_PER_SLICE . 3)
(CRAM_OPT_SLICES_PER_CONTAINER . 4)
(CRAM_OPT_RANGE . 5)
(CRAM_OPT_VERSION . 6)
(CRAM_OPT_EMBED_REF . 7)
(CRAM_OPT_IGNORE_MD5 . 8)
(CRAM_OPT_REFERENCE . 9)
(CRAM_OPT_MULTI_SEQ_PER_SLICE . 10)
(CRAM_OPT_NO_REF . 11)
(CRAM_OPT_USE_BZIP2 . 12)
(CRAM_OPT_SHARED_REF . 13)
(CRAM_OPT_NTHREADS . 14)
(CRAM_OPT_THREAD_POOL . 15)
(CRAM_OPT_USE_LZMA . 16)
(CRAM_OPT_USE_RANS . 17)
(CRAM_OPT_REQUIRED_FIELDS . 18)
(CRAM_OPT_LOSSY_NAMES . 19)
(CRAM_OPT_BASES_PER_SLICE . 20)
(HTS_OPT_COMPRESSION_LEVEL . 100)
(HTS_OPT_NTHREADS . 101)
(HTS_OPT_THREAD_POOL . 102)
(HTS_OPT_CACHE_SIZE . 103)
(HTS_OPT_BLOCK_SIZE . 104))
)
(define enum-hts_fmt_option-enum-vnl
(map (lambda (pair) (cons (cdr pair) (car pair)))
enum-hts_fmt_option-enum-nvl))
(define-public (unwrap-enum-hts_fmt_option n)
(cond
((symbol? n)
(or (assq-ref enum-hts_fmt_option-enum-nvl n) (error "bad arg")))
((integer? n) n)
(else (error "bad arg"))))
(define-public (wrap-enum-hts_fmt_option v)
(assq-ref enum-hts_fmt_option-enum-vnl v))
;; typedef struct hts_opt {
;; char *arg; /* string form, strdup()ed*/
;; enum hts_fmt_option opt; /* tokenised key*/
;; union {
;; int i;
;; char *s;
;; } val;
;; struct hts_opt *next;
;; } hts_opt;
;; == hts_opt =>
(define-public hts_opt-desc
(bs:struct
(list `(arg ,(bs:pointer int8))
`(opt ,int)
`(val ,(bs:union
(list `(i ,int) `(s ,(bs:pointer int8)))))
`(next ,(bs:pointer 'void)))))
(define-fh-compound-type hts_opt hts_opt-desc hts_opt? make-hts_opt)
(export hts_opt hts_opt? make-hts_opt)
(define-public hts_opt*-desc
(bs:pointer hts_opt-desc))
(define-fh-pointer-type hts_opt* hts_opt*-desc hts_opt*? make-hts_opt*)
(export hts_opt* hts_opt*? make-hts_opt*)
(ref<->deref!
hts_opt*
make-hts_opt*
hts_opt
make-hts_opt)
;; == struct-hts_opt =>
(define-public struct-hts_opt-desc hts_opt-desc)
(define-fh-compound-type struct-hts_opt struct-hts_opt-desc struct-hts_opt?
make-struct-hts_opt)
(export struct-hts_opt struct-hts_opt? make-struct-hts_opt)
(define-public struct-hts_opt*-desc
hts_opt*-desc)
(define-fh-pointer-type struct-hts_opt* struct-hts_opt*-desc struct-hts_opt*?
make-struct-hts_opt*)
(export struct-hts_opt* struct-hts_opt*? make-struct-hts_opt*)
(ref<->deref!
struct-hts_opt*
make-struct-hts_opt*
struct-hts_opt
make-struct-hts_opt)
;; int hts_opt_add(hts_opt **opts, const char *c_arg);
(define ~hts_opt_add
(delay (fh-link-proc
"hts_opt_add"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_opt_add opts c_arg)
(let ((~opts (unwrap~pointer opts))
(~c_arg (unwrap~pointer c_arg)))
((force ~hts_opt_add) ~opts ~c_arg)))
(export hts_opt_add)
;; int hts_opt_apply(htsFile *fp, hts_opt *opts);
(define ~hts_opt_apply
(delay (fh-link-proc
"hts_opt_apply"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_opt_apply fp opts)
(let ((~fp ((fht-unwrap htsFile*) fp))
(~opts ((fht-unwrap hts_opt*) opts)))
((force ~hts_opt_apply) ~fp ~opts)))
(export hts_opt_apply)
;; void hts_opt_free(hts_opt *opts);
(define ~hts_opt_free
(delay (fh-link-proc
"hts_opt_free"
ffi:void
(list ffi-void*)
link-lib)))
(define (hts_opt_free opts)
(let ((~opts ((fht-unwrap hts_opt*) opts)))
((force ~hts_opt_free) ~opts)))
(export hts_opt_free)
;; int hts_parse_format(htsFormat *opt, const char *str);
(define ~hts_parse_format
(delay (fh-link-proc
"hts_parse_format"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_parse_format opt str)
(let ((~opt ((fht-unwrap htsFormat*) opt))
(~str (unwrap~pointer str)))
((force ~hts_parse_format) ~opt ~str)))
(export hts_parse_format)
;; int hts_parse_opt_list(htsFormat *opt, const char *str);
(define ~hts_parse_opt_list
(delay (fh-link-proc
"hts_parse_opt_list"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_parse_opt_list opt str)
(let ((~opt ((fht-unwrap htsFormat*) opt))
(~str (unwrap~pointer str)))
((force ~hts_parse_opt_list) ~opt ~str)))
(export hts_parse_opt_list)
;; extern const unsigned char seq_nt16_table[256];
(define seq_nt16_table
(let* ((addr #f)
(memoize-addr
(lambda ()
(unless
addr
(set! addr
(make-bytestructure
(ffi:pointer->bytevector
(dynamic-pointer "seq_nt16_table" (dynamic-link))
(ffi:sizeof '*))
0
(bs:pointer (bs:vector 256 uint8))))))))
(case-lambda
(() (memoize-addr) (bytestructure-ref addr '*)))))
(export seq_nt16_table)
;; extern const char seq_nt16_str[];
(define seq_nt16_str
(let* ((addr #f)
(memoize-addr
(lambda ()
(unless
addr
(set! addr
(make-bytestructure
(ffi:pointer->bytevector
(dynamic-pointer "seq_nt16_str" (dynamic-link))
(ffi:sizeof '*))
0
(bs:pointer (bs:pointer int8))))))))
(case-lambda
(() (memoize-addr) (bytestructure-ref addr '*)))))
(export seq_nt16_str)
;; extern const int seq_nt16_int[];
(define seq_nt16_int
(let* ((addr #f)
(memoize-addr
(lambda ()
(unless
addr
(set! addr
(make-bytestructure
(ffi:pointer->bytevector
(dynamic-pointer "seq_nt16_int" (dynamic-link))
(ffi:sizeof '*))
0
(bs:pointer (bs:pointer int))))))))
(case-lambda
(() (memoize-addr) (bytestructure-ref addr '*)))))
(export seq_nt16_int)
;; const char *hts_version(void);
(define ~hts_version
(delay (fh-link-proc
"hts_version"
ffi-void*
(list)
link-lib)))
(define (hts_version)
(let () ((force ~hts_version))))
(export hts_version)
;; int hts_detect_format(struct hFILE *fp, htsFormat *fmt);
(define ~hts_detect_format
(delay (fh-link-proc
"hts_detect_format"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_detect_format fp fmt)
(let ((~fp (unwrap~pointer fp))
(~fmt ((fht-unwrap htsFormat*) fmt)))
((force ~hts_detect_format) ~fp ~fmt)))
(export hts_detect_format)
;; char *hts_format_description(const htsFormat *format);
(define ~hts_format_description
(delay (fh-link-proc
"hts_format_description"
ffi-void*
(list ffi-void*)
link-lib)))
(define (hts_format_description format)
(let ((~format ((fht-unwrap htsFormat*) format)))
((force ~hts_format_description) ~format)))
(export hts_format_description)
;; htsFile *hts_open(const char *fn, const char *mode);
(define ~hts_open
(delay (fh-link-proc
"hts_open"
ffi-void*
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_open fn mode)
(let ((~fn (unwrap~pointer fn))
(~mode (unwrap~pointer mode)))
((fht-wrap htsFile*)
((force ~hts_open) ~fn ~mode))))
(export hts_open)
;; htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *
;; fmt);
(define ~hts_open_format
(delay (fh-link-proc
"hts_open_format"
ffi-void*
(list ffi-void* ffi-void* ffi-void*)
link-lib)))
(define (hts_open_format fn mode fmt)
(let ((~fn (unwrap~pointer fn))
(~mode (unwrap~pointer mode))
(~fmt ((fht-unwrap htsFormat*) fmt)))
((fht-wrap htsFile*)
((force ~hts_open_format) ~fn ~mode ~fmt))))
(export hts_open_format)
;; htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode);
(define ~hts_hopen
(delay (fh-link-proc
"hts_hopen"
ffi-void*
(list ffi-void* ffi-void* ffi-void*)
link-lib)))
(define (hts_hopen fp fn mode)
(let ((~fp (unwrap~pointer fp))
(~fn (unwrap~pointer fn))
(~mode (unwrap~pointer mode)))
((fht-wrap htsFile*)
((force ~hts_hopen) ~fp ~fn ~mode))))
(export hts_hopen)
;; int hts_close(htsFile *fp);
(define ~hts_close
(delay (fh-link-proc
"hts_close"
ffi:int
(list ffi-void*)
link-lib)))
(define (hts_close fp)
(let ((~fp ((fht-unwrap htsFile*) fp)))
((force ~hts_close) ~fp)))
(export hts_close)
;; const htsFormat *hts_get_format(htsFile *fp);
(define ~hts_get_format
(delay (fh-link-proc
"hts_get_format"
ffi-void*
(list ffi-void*)
link-lib)))
(define (hts_get_format fp)
(let ((~fp ((fht-unwrap htsFile*) fp)))
((fht-wrap htsFormat*)
((force ~hts_get_format) ~fp))))
(export hts_get_format)
;; const char *hts_format_file_extension(const htsFormat *format);
(define ~hts_format_file_extension
(delay (fh-link-proc
"hts_format_file_extension"
ffi-void*
(list ffi-void*)
link-lib)))
(define (hts_format_file_extension format)
(let ((~format ((fht-unwrap htsFormat*) format)))
((force ~hts_format_file_extension) ~format)))
(export hts_format_file_extension)
;; int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...);
;; ... failed.
;; int hts_getline(htsFile *fp, int delimiter, kstring_t *str);
(define ~hts_getline
(delay (fh-link-proc
"hts_getline"
ffi:int
(list ffi-void* ffi:int ffi-void*)
link-lib)))
(define (hts_getline fp delimiter str)
(let ((~fp ((fht-unwrap htsFile*) fp))
(~delimiter (unwrap~fixed delimiter))
(~str ((fht-unwrap kstring_t*) str)))
((force ~hts_getline) ~fp ~delimiter ~str)))
(export hts_getline)
;; char **hts_readlines(const char *fn, int *_n);
(define ~hts_readlines
(delay (fh-link-proc
"hts_readlines"
ffi-void*
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_readlines fn _n)
(let ((~fn (unwrap~pointer fn))
(~_n (unwrap~pointer _n)))
((force ~hts_readlines) ~fn ~_n)))
(export hts_readlines)
;; char **hts_readlist(const char *fn, int is_file, int *_n);
(define ~hts_readlist
(delay (fh-link-proc
"hts_readlist"
ffi-void*
(list ffi-void* ffi:int ffi-void*)
link-lib)))
(define (hts_readlist fn is_file _n)
(let ((~fn (unwrap~pointer fn))
(~is_file (unwrap~fixed is_file))
(~_n (unwrap~pointer _n)))
((force ~hts_readlist) ~fn ~is_file ~_n)))
(export hts_readlist)
;; int hts_set_threads(htsFile *fp, int n);
(define ~hts_set_threads
(delay (fh-link-proc
"hts_set_threads"
ffi:int
(list ffi-void* ffi:int)
link-lib)))
(define (hts_set_threads fp n)
(let ((~fp ((fht-unwrap htsFile*) fp))
(~n (unwrap~fixed n)))
((force ~hts_set_threads) ~fp ~n)))
(export hts_set_threads)
;; int hts_set_thread_pool(htsFile *fp, htsThreadPool *p);
(define ~hts_set_thread_pool
(delay (fh-link-proc
"hts_set_thread_pool"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_set_thread_pool fp p)
(let ((~fp ((fht-unwrap htsFile*) fp))
(~p ((fht-unwrap htsThreadPool*) p)))
((force ~hts_set_thread_pool) ~fp ~p)))
(export hts_set_thread_pool)
;; void hts_set_cache_size(htsFile *fp, int n);
(define ~hts_set_cache_size
(delay (fh-link-proc
"hts_set_cache_size"
ffi:void
(list ffi-void* ffi:int)
link-lib)))
(define (hts_set_cache_size fp n)
(let ((~fp ((fht-unwrap htsFile*) fp))
(~n (unwrap~fixed n)))
((force ~hts_set_cache_size) ~fp ~n)))
(export hts_set_cache_size)
;; int hts_set_fai_filename(htsFile *fp, const char *fn_aux);
(define ~hts_set_fai_filename
(delay (fh-link-proc
"hts_set_fai_filename"
ffi:int
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_set_fai_filename fp fn_aux)
(let ((~fp ((fht-unwrap htsFile*) fp))
(~fn_aux (unwrap~pointer fn_aux)))
((force ~hts_set_fai_filename) ~fp ~fn_aux)))
(export hts_set_fai_filename)
;; int hts_check_EOF(htsFile *fp);
(define ~hts_check_EOF
(delay (fh-link-proc
"hts_check_EOF"
ffi:int
(list ffi-void*)
link-lib)))
(define (hts_check_EOF fp)
(let ((~fp ((fht-unwrap htsFile*) fp)))
((force ~hts_check_EOF) ~fp)))
(export hts_check_EOF)
;; typedef struct __hts_idx_t hts_idx_t;
(define-public hts_idx_t-desc 'void)
(define-public hts_idx_t*-desc (bs:pointer hts_idx_t-desc))
(define-fh-pointer-type hts_idx_t* hts_idx_t*-desc hts_idx_t*? make-hts_idx_t*
)
(export hts_idx_t* hts_idx_t*? make-hts_idx_t*)
;; typedef struct {
;; uint64_t u, v;
;; } hts_pair64_t;
(define-public hts_pair64_t-desc
(bs:struct (list `(v ,uint64) `(u ,uint64))))
(define-fh-compound-type hts_pair64_t hts_pair64_t-desc hts_pair64_t?
make-hts_pair64_t)
(export hts_pair64_t hts_pair64_t? make-hts_pair64_t)
(define-public hts_pair64_t*-desc
(bs:pointer hts_pair64_t-desc))
(define-fh-pointer-type hts_pair64_t* hts_pair64_t*-desc hts_pair64_t*?
make-hts_pair64_t*)
(export hts_pair64_t* hts_pair64_t*? make-hts_pair64_t*)
(ref<->deref!
hts_pair64_t*
make-hts_pair64_t*
hts_pair64_t
make-hts_pair64_t)
;; typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *
;; beg, int *end);
(define ~hts_readrec_func
(delay (fh-link-proc
"hts_readrec_func"
ffi:int
(list ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*)
link-lib)))
(define (hts_readrec_func fp data r tid beg end)
(let ((~fp ((fht-unwrap BGZF*) fp))
(~data (unwrap~pointer data))
(~r (unwrap~pointer r))
(~tid (unwrap~pointer tid))
(~beg (unwrap~pointer beg))
(~end (unwrap~pointer end)))
((force ~hts_readrec_func)
~fp
~data
~r
~tid
~beg
~end)))
(export hts_readrec_func)
;; typedef struct {
;; uint32_t read_rest : 1, finished : 1, is_cram : 1, dummy : 29;
;; int tid, beg, end, n_off, i;
;; int curr_tid, curr_beg, curr_end;
;; uint64_t curr_off;
;; hts_pair64_t *off;
;; hts_readrec_func *readrec;
;; struct {
;; int n, m;
;; int *a;
;; } bins;
;; } hts_itr_t;
(define-public hts_itr_t-desc
(bs:struct
(list `(dummy ,uint64 29)
`(is_cram ,uint64 1)
`(finished ,uint64 1)
`(read_rest ,uint64 1)
`(i ,int)
`(n_off ,int)
`(end ,int)
`(beg ,int)
`(tid ,int)
`(curr_end ,int)
`(curr_beg ,int)
`(curr_tid ,int)
`(curr_off ,uint64)
`(off ,hts_pair64_t*-desc)
`(readrec ,(bs:pointer 'void))
`(bins ,(bs:struct
(list `(m ,int) `(n ,int) `(a ,(bs:pointer int))))))))
(define-fh-compound-type hts_itr_t hts_itr_t-desc hts_itr_t? make-hts_itr_t)
(export hts_itr_t hts_itr_t? make-hts_itr_t)
(define-public hts_itr_t*-desc
(bs:pointer hts_itr_t-desc))
(define-fh-pointer-type hts_itr_t* hts_itr_t*-desc hts_itr_t*? make-hts_itr_t*
)
(export hts_itr_t* hts_itr_t*? make-hts_itr_t*)
(ref<->deref!
hts_itr_t*
make-hts_itr_t*
hts_itr_t
make-hts_itr_t)
;; hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int
;; n_lvls);
(define ~hts_idx_init
(delay (fh-link-proc
"hts_idx_init"
ffi-void*
(list ffi:int ffi:int ffi:uint64 ffi:int ffi:int)
link-lib)))
(define (hts_idx_init n fmt offset0 min_shift n_lvls)
(let ((~n (unwrap~fixed n))
(~fmt (unwrap~fixed fmt))
(~offset0 (unwrap~fixed offset0))
(~min_shift (unwrap~fixed min_shift))
(~n_lvls (unwrap~fixed n_lvls)))
((fht-wrap hts_idx_t*)
((force ~hts_idx_init)
~n
~fmt
~offset0
~min_shift
~n_lvls))))
(export hts_idx_init)
;; void hts_idx_destroy(hts_idx_t *idx);
(define ~hts_idx_destroy
(delay (fh-link-proc
"hts_idx_destroy"
ffi:void
(list ffi-void*)
link-lib)))
(define (hts_idx_destroy idx)
(let ((~idx ((fht-unwrap hts_idx_t*) idx)))
((force ~hts_idx_destroy) ~idx)))
(export hts_idx_destroy)
;; int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset
;; , int is_mapped);
(define ~hts_idx_push
(delay (fh-link-proc
"hts_idx_push"
ffi:int
(list ffi-void*
ffi:int
ffi:int
ffi:int
ffi:uint64
ffi:int)
link-lib)))
(define (hts_idx_push idx tid beg end offset is_mapped)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~tid (unwrap~fixed tid))
(~beg (unwrap~fixed beg))
(~end (unwrap~fixed end))
(~offset (unwrap~fixed offset))
(~is_mapped (unwrap~fixed is_mapped)))
((force ~hts_idx_push)
~idx
~tid
~beg
~end
~offset
~is_mapped)))
(export hts_idx_push)
;; void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset);
(define ~hts_idx_finish
(delay (fh-link-proc
"hts_idx_finish"
ffi:void
(list ffi-void* ffi:uint64)
link-lib)))
(define (hts_idx_finish idx final_offset)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~final_offset (unwrap~fixed final_offset)))
((force ~hts_idx_finish) ~idx ~final_offset)))
(export hts_idx_finish)
;; int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt);
(define ~hts_idx_save
(delay (fh-link-proc
"hts_idx_save"
ffi:int
(list ffi-void* ffi-void* ffi:int)
link-lib)))
(define (hts_idx_save idx fn fmt)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~fn (unwrap~pointer fn))
(~fmt (unwrap~fixed fmt)))
((force ~hts_idx_save) ~idx ~fn ~fmt)))
(export hts_idx_save)
;; int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx
;; , int fmt);
(define ~hts_idx_save_as
(delay (fh-link-proc
"hts_idx_save_as"
ffi:int
(list ffi-void* ffi-void* ffi-void* ffi:int)
link-lib)))
(define (hts_idx_save_as idx fn fnidx fmt)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~fn (unwrap~pointer fn))
(~fnidx (unwrap~pointer fnidx))
(~fmt (unwrap~fixed fmt)))
((force ~hts_idx_save_as) ~idx ~fn ~fnidx ~fmt)))
(export hts_idx_save_as)
;; hts_idx_t *hts_idx_load(const char *fn, int fmt);
(define ~hts_idx_load
(delay (fh-link-proc
"hts_idx_load"
ffi-void*
(list ffi-void* ffi:int)
link-lib)))
(define (hts_idx_load fn fmt)
(let ((~fn (unwrap~pointer fn))
(~fmt (unwrap~fixed fmt)))
((fht-wrap hts_idx_t*)
((force ~hts_idx_load) ~fn ~fmt))))
(export hts_idx_load)
;; hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);
(define ~hts_idx_load2
(delay (fh-link-proc
"hts_idx_load2"
ffi-void*
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_idx_load2 fn fnidx)
(let ((~fn (unwrap~pointer fn))
(~fnidx (unwrap~pointer fnidx)))
((fht-wrap hts_idx_t*)
((force ~hts_idx_load2) ~fn ~fnidx))))
(export hts_idx_load2)
;; uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta);
(define ~hts_idx_get_meta
(delay (fh-link-proc
"hts_idx_get_meta"
ffi-void*
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_idx_get_meta idx l_meta)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~l_meta (unwrap~pointer l_meta)))
((force ~hts_idx_get_meta) ~idx ~l_meta)))
(export hts_idx_get_meta)
;; int hts_idx_set_meta(hts_idx_t *idx, uint32_t l_meta, uint8_t *meta, int
;; is_copy);
(define ~hts_idx_set_meta
(delay (fh-link-proc
"hts_idx_set_meta"
ffi:int
(list ffi-void* ffi:uint32 ffi-void* ffi:int)
link-lib)))
(define (hts_idx_set_meta idx l_meta meta is_copy)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~l_meta (unwrap~fixed l_meta))
(~meta (unwrap~pointer meta))
(~is_copy (unwrap~fixed is_copy)))
((force ~hts_idx_set_meta)
~idx
~l_meta
~meta
~is_copy)))
(export hts_idx_set_meta)
;; int hts_idx_get_stat(const hts_idx_t *idx, int tid, uint64_t *mapped,
;; uint64_t *unmapped);
(define ~hts_idx_get_stat
(delay (fh-link-proc
"hts_idx_get_stat"
ffi:int
(list ffi-void* ffi:int ffi-void* ffi-void*)
link-lib)))
(define (hts_idx_get_stat idx tid mapped unmapped)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~tid (unwrap~fixed tid))
(~mapped (unwrap~pointer mapped))
(~unmapped (unwrap~pointer unmapped)))
((force ~hts_idx_get_stat)
~idx
~tid
~mapped
~unmapped)))
(export hts_idx_get_stat)
;; uint64_t hts_idx_get_n_no_coor(const hts_idx_t *idx);
(define ~hts_idx_get_n_no_coor
(delay (fh-link-proc
"hts_idx_get_n_no_coor"
ffi:uint64
(list ffi-void*)
link-lib)))
(define (hts_idx_get_n_no_coor idx)
(let ((~idx ((fht-unwrap hts_idx_t*) idx)))
((force ~hts_idx_get_n_no_coor) ~idx)))
(export hts_idx_get_n_no_coor)
;; long long hts_parse_decimal(const char *str, char **strend, int flags);
(define ~hts_parse_decimal
(delay (fh-link-proc
"hts_parse_decimal"
ffi:long
(list ffi-void* ffi-void* ffi:int)
link-lib)))
(define (hts_parse_decimal str strend flags)
(let ((~str (unwrap~pointer str))
(~strend (unwrap~pointer strend))
(~flags (unwrap~fixed flags)))
((force ~hts_parse_decimal) ~str ~strend ~flags)))
(export hts_parse_decimal)
;; const char *hts_parse_reg(const char *str, int *beg, int *end);
(define ~hts_parse_reg
(delay (fh-link-proc
"hts_parse_reg"
ffi-void*
(list ffi-void* ffi-void* ffi-void*)
link-lib)))
(define (hts_parse_reg str beg end)
(let ((~str (unwrap~pointer str))
(~beg (unwrap~pointer beg))
(~end (unwrap~pointer end)))
((force ~hts_parse_reg) ~str ~beg ~end)))
(export hts_parse_reg)
;; hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end,
;; hts_readrec_func *readrec);
(define ~hts_itr_query
(delay (fh-link-proc
"hts_itr_query"
ffi-void*
(list ffi-void*
ffi:int
ffi:int
ffi:int
ffi-void*)
link-lib)))
(define (hts_itr_query idx tid beg end readrec)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~tid (unwrap~fixed tid))
(~beg (unwrap~fixed beg))
(~end (unwrap~fixed end))
(~readrec
((make-fctn-param-unwrapper
ffi:int
(list ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*))
readrec)))
((fht-wrap hts_itr_t*)
((force ~hts_itr_query)
~idx
~tid
~beg
~end
~readrec))))
(export hts_itr_query)
;; void hts_itr_destroy(hts_itr_t *iter);
(define ~hts_itr_destroy
(delay (fh-link-proc
"hts_itr_destroy"
ffi:void
(list ffi-void*)
link-lib)))
(define (hts_itr_destroy iter)
(let ((~iter ((fht-unwrap hts_itr_t*) iter)))
((force ~hts_itr_destroy) ~iter)))
(export hts_itr_destroy)
;; typedef int (*hts_name2id_f)(void *, const char *);
(define-public hts_name2id_f-desc
(bs:pointer
(delay (fh:function ffi:int (list ffi-void* ffi-void*))))
)
(define-fh-function*-type
hts_name2id_f
hts_name2id_f-desc
hts_name2id_f?
make-hts_name2id_f)
(export hts_name2id_f hts_name2id_f? make-hts_name2id_f)
;; typedef const char *(*hts_id2name_f)(void *, int);
(define-public hts_id2name_f-desc
(bs:pointer
(delay (fh:function ffi-void* (list ffi-void* ffi:int))))
)
(define-fh-function*-type
hts_id2name_f
hts_id2name_f-desc
hts_id2name_f?
make-hts_id2name_f)
(export hts_id2name_f hts_id2name_f? make-hts_id2name_f)
;; typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, int beg
;; , int end, hts_readrec_func *readrec);
(define ~hts_itr_query_func
(delay (fh-link-proc
"hts_itr_query_func"
ffi-void*
(list ffi-void*
ffi:int
ffi:int
ffi:int
ffi-void*)
link-lib)))
(define (hts_itr_query_func idx tid beg end readrec)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~tid (unwrap~fixed tid))
(~beg (unwrap~fixed beg))
(~end (unwrap~fixed end))
(~readrec
((make-fctn-param-unwrapper
ffi:int
(list ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*))
readrec)))
((fht-wrap hts_itr_t*)
((force ~hts_itr_query_func)
~idx
~tid
~beg
~end
~readrec))))
(export hts_itr_query_func)
;; hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg,
;; hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query,
;; hts_readrec_func *readrec);
(define ~hts_itr_querys
(delay (fh-link-proc
"hts_itr_querys"
ffi-void*
(list ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*)
link-lib)))
(define (hts_itr_querys
idx
reg
getid
hdr
itr_query
readrec)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~reg (unwrap~pointer reg))
(~getid ((fht-unwrap hts_name2id_f) getid))
(~hdr (unwrap~pointer hdr))
(~itr_query
((make-fctn-param-unwrapper
ffi-void*
(list ffi-void*
ffi:int
ffi:int
ffi:int
ffi-void*))
itr_query))
(~readrec
((make-fctn-param-unwrapper
ffi:int
(list ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*
ffi-void*))
readrec)))
((fht-wrap hts_itr_t*)
((force ~hts_itr_querys)
~idx
~reg
~getid
~hdr
~itr_query
~readrec))))
(export hts_itr_querys)
;; int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data);
(define ~hts_itr_next
(delay (fh-link-proc
"hts_itr_next"
ffi:int
(list ffi-void* ffi-void* ffi-void* ffi-void*)
link-lib)))
(define (hts_itr_next fp iter r data)
(let ((~fp ((fht-unwrap BGZF*) fp))
(~iter ((fht-unwrap hts_itr_t*) iter))
(~r (unwrap~pointer r))
(~data (unwrap~pointer data)))
((force ~hts_itr_next) ~fp ~iter ~r ~data)))
(export hts_itr_next)
;; const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f
;; getid, void *hdr); /* free only the array, not the values*/
(define ~hts_idx_seqnames
(delay (fh-link-proc
"hts_idx_seqnames"
ffi-void*
(list ffi-void* ffi-void* ffi-void* ffi-void*)
link-lib)))
(define (hts_idx_seqnames idx n getid hdr)
(let ((~idx ((fht-unwrap hts_idx_t*) idx))
(~n (unwrap~pointer n))
(~getid ((fht-unwrap hts_id2name_f) getid))
(~hdr (unwrap~pointer hdr)))
((force ~hts_idx_seqnames) ~idx ~n ~getid ~hdr)))
(export hts_idx_seqnames)
;; int hts_file_type(const char *fname);
(define ~hts_file_type
(delay (fh-link-proc
"hts_file_type"
ffi:int
(list ffi-void*)
link-lib)))
(define (hts_file_type fname)
(let ((~fname (unwrap~pointer fname)))
((force ~hts_file_type) ~fname)))
(export hts_file_type)
;; typedef struct errmod_t errmod_t;
(define-public errmod_t-desc 'void)
(define-public errmod_t*-desc (bs:pointer errmod_t-desc))
(define-fh-pointer-type errmod_t* errmod_t*-desc errmod_t*? make-errmod_t*)
(export errmod_t* errmod_t*? make-errmod_t*)
;; errmod_t *errmod_init(double depcorr);
(define ~errmod_init
(delay (fh-link-proc
"errmod_init"
ffi-void*
(list ffi:double)
link-lib)))
(define (errmod_init depcorr)
(let ((~depcorr (unwrap~float depcorr)))
((fht-wrap errmod_t*)
((force ~errmod_init) ~depcorr))))
(export errmod_init)
;; void errmod_destroy(errmod_t *em);
(define ~errmod_destroy
(delay (fh-link-proc
"errmod_destroy"
ffi:void
(list ffi-void*)
link-lib)))
(define (errmod_destroy em)
(let ((~em ((fht-unwrap errmod_t*) em)))
((force ~errmod_destroy) ~em)))
(export errmod_destroy)
;; int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q)
;; ;
(define ~errmod_cal
(delay (fh-link-proc
"errmod_cal"
ffi:int
(list ffi-void*
ffi:int
ffi:int
ffi-void*
ffi-void*)
link-lib)))
(define (errmod_cal em n m bases q)
(let ((~em ((fht-unwrap errmod_t*) em))
(~n (unwrap~fixed n))
(~m (unwrap~fixed m))
(~bases (unwrap~pointer bases))
(~q (unwrap~pointer q)))
((force ~errmod_cal) ~em ~n ~m ~bases ~q)))
(export errmod_cal)
;; typedef struct probaln_par_t {
;; float d, e;
;; int bw;
;; } probaln_par_t;
;; == probaln_par_t =>
(define-public probaln_par_t-desc
(bs:struct
(list `(e ,float) `(d ,float) `(bw ,int))))
(define-fh-compound-type probaln_par_t probaln_par_t-desc probaln_par_t?
make-probaln_par_t)
(export probaln_par_t probaln_par_t? make-probaln_par_t)
(define-public probaln_par_t*-desc
(bs:pointer probaln_par_t-desc))
(define-fh-pointer-type probaln_par_t* probaln_par_t*-desc probaln_par_t*?
make-probaln_par_t*)
(export probaln_par_t* probaln_par_t*? make-probaln_par_t*)
(ref<->deref!
probaln_par_t*
make-probaln_par_t*
probaln_par_t
make-probaln_par_t)
;; == struct-probaln_par_t =>
(define-public struct-probaln_par_t-desc
probaln_par_t-desc)
(define-fh-compound-type struct-probaln_par_t struct-probaln_par_t-desc
struct-probaln_par_t? make-struct-probaln_par_t)
(export struct-probaln_par_t struct-probaln_par_t? make-struct-probaln_par_t)
(define-public struct-probaln_par_t*-desc
probaln_par_t*-desc)
(define-fh-pointer-type struct-probaln_par_t* struct-probaln_par_t*-desc
struct-probaln_par_t*? make-struct-probaln_par_t*)
(export struct-probaln_par_t* struct-probaln_par_t*?
make-struct-probaln_par_t*)
(ref<->deref!
struct-probaln_par_t*
make-struct-probaln_par_t*
struct-probaln_par_t
make-struct-probaln_par_t)
;; int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int
;; l_query, const uint8_t *iqual, const probaln_par_t *c, int *state,
;; uint8_t *q);
(define ~probaln_glocal
(delay (fh-link-proc
"probaln_glocal"
ffi:int
(list ffi-void*
ffi:int
ffi-void*
ffi:int
ffi-void*
ffi-void*
ffi-void*
ffi-void*)
link-lib)))
(define (probaln_glocal
ref
l_ref
query
l_query
iqual
c
state
q)
(let ((~ref (unwrap~pointer ref))
(~l_ref (unwrap~fixed l_ref))
(~query (unwrap~pointer query))
(~l_query (unwrap~fixed l_query))
(~iqual (unwrap~pointer iqual))
(~c ((fht-unwrap probaln_par_t*) c))
(~state (unwrap~pointer state))
(~q (unwrap~pointer q)))
((force ~probaln_glocal)
~ref
~l_ref
~query
~l_query
~iqual
~c
~state
~q)))
(export probaln_glocal)
;; typedef struct hts_md5_context hts_md5_context;
(define-public hts_md5_context-desc 'void)
(define-public hts_md5_context*-desc (bs:pointer hts_md5_context-desc))
(define-fh-pointer-type hts_md5_context* hts_md5_context*-desc
hts_md5_context*? make-hts_md5_context*)
(export hts_md5_context* hts_md5_context*? make-hts_md5_context*)
;; hts_md5_context *hts_md5_init(void);
(define ~hts_md5_init
(delay (fh-link-proc
"hts_md5_init"
ffi-void*
(list)
link-lib)))
(define (hts_md5_init)
(let ()
((fht-wrap hts_md5_context*)
((force ~hts_md5_init)))))
(export hts_md5_init)
;; void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long
;; size);
(define ~hts_md5_update
(delay (fh-link-proc
"hts_md5_update"
ffi:void
(list ffi-void* ffi-void* ffi:unsigned-long)
link-lib)))
(define (hts_md5_update ctx data size)
(let ((~ctx ((fht-unwrap hts_md5_context*) ctx))
(~data (unwrap~pointer data))
(~size (unwrap~fixed size)))
((force ~hts_md5_update) ~ctx ~data ~size)))
(export hts_md5_update)
;; void hts_md5_final(unsigned char *digest, hts_md5_context *ctx);
(define ~hts_md5_final
(delay (fh-link-proc
"hts_md5_final"
ffi:void
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_md5_final digest ctx)
(let ((~digest (unwrap~pointer digest))
(~ctx ((fht-unwrap hts_md5_context*) ctx)))
((force ~hts_md5_final) ~digest ~ctx)))
(export hts_md5_final)
;; void hts_md5_reset(hts_md5_context *ctx);
(define ~hts_md5_reset
(delay (fh-link-proc
"hts_md5_reset"
ffi:void
(list ffi-void*)
link-lib)))
(define (hts_md5_reset ctx)
(let ((~ctx ((fht-unwrap hts_md5_context*) ctx)))
((force ~hts_md5_reset) ~ctx)))
(export hts_md5_reset)
;; void hts_md5_hex(char *hex, const unsigned char *digest);
(define ~hts_md5_hex
(delay (fh-link-proc
"hts_md5_hex"
ffi:void
(list ffi-void* ffi-void*)
link-lib)))
(define (hts_md5_hex hex digest)
(let ((~hex (unwrap~pointer hex))
(~digest (unwrap~pointer digest)))
((force ~hts_md5_hex) ~hex ~digest)))
(export hts_md5_hex)
;; void hts_md5_destroy(hts_md5_context *ctx);
(define ~hts_md5_destroy
(delay (fh-link-proc
"hts_md5_destroy"
ffi:void
(list ffi-void*)
link-lib)))
(define (hts_md5_destroy ctx)
(let ((~ctx ((fht-unwrap hts_md5_context*) ctx)))
((force ~hts_md5_destroy) ~ctx)))
(export hts_md5_destroy)
;; access to enum symbols and #define'd constants:
(define ffi-htslib-symbol-val
(let ((sym-tab
'((HTS_LOG_OFF . 0)
(HTS_LOG_ERROR . 1)
(HTS_LOG_WARNING . 3)
(HTS_LOG_INFO . 4)
(HTS_LOG_DEBUG . 5)
(HTS_LOG_TRACE . 6)
(unknown_category . 0)
(sequence_data . 1)
(variant_data . 2)
(index_file . 3)
(region_list . 4)
(category_maximum . 32767)
(unknown_format . 0)
(binary_format . 1)
(text_format . 2)
(sam . 3)
(bam . 4)
(bai . 5)
(cram . 6)
(crai . 7)
(vcf . 8)
(bcf . 9)
(csi . 10)
(gzi . 11)
(tbi . 12)
(bed . 13)
(htsget . 14)
(json . 14)
(format_maximum . 32767)
(no_compression . 0)
(gzip . 1)
(bgzf . 2)
(custom . 3)
(compression_maximum . 32767)
(SAM_QNAME . 1)
(SAM_FLAG . 2)
(SAM_RNAME . 4)
(SAM_POS . 8)
(SAM_MAPQ . 16)
(SAM_CIGAR . 32)
(SAM_RNEXT . 64)
(SAM_PNEXT . 128)
(SAM_TLEN . 256)
(SAM_SEQ . 512)
(SAM_QUAL . 1024)
(SAM_AUX . 2048)
(SAM_RGAUX . 4096)
(CRAM_OPT_DECODE_MD . 0)
(CRAM_OPT_PREFIX . 1)
(CRAM_OPT_VERBOSITY . 2)
(CRAM_OPT_SEQS_PER_SLICE . 3)
(CRAM_OPT_SLICES_PER_CONTAINER . 4)
(CRAM_OPT_RANGE . 5)
(CRAM_OPT_VERSION . 6)
(CRAM_OPT_EMBED_REF . 7)
(CRAM_OPT_IGNORE_MD5 . 8)
(CRAM_OPT_REFERENCE . 9)
(CRAM_OPT_MULTI_SEQ_PER_SLICE . 10)
(CRAM_OPT_NO_REF . 11)
(CRAM_OPT_USE_BZIP2 . 12)
(CRAM_OPT_SHARED_REF . 13)
(CRAM_OPT_NTHREADS . 14)
(CRAM_OPT_THREAD_POOL . 15)
(CRAM_OPT_USE_LZMA . 16)
(CRAM_OPT_USE_RANS . 17)
(CRAM_OPT_REQUIRED_FIELDS . 18)
(CRAM_OPT_LOSSY_NAMES . 19)
(CRAM_OPT_BASES_PER_SLICE . 20)
(HTS_OPT_COMPRESSION_LEVEL . 100)
(HTS_OPT_NTHREADS . 101)
(HTS_OPT_THREAD_POOL . 102)
(HTS_OPT_CACHE_SIZE . 103)
(HTS_OPT_BLOCK_SIZE . 104)
(HTS_FMT_CSI . 0)
(HTS_FMT_BAI . 1)
(HTS_FMT_TBI . 2)
(HTS_FMT_CRAI . 3)
(HTS_PARSE_THOUSANDS_SEP . 1)
(FT_UNKN . 0)
(FT_GZ . 1)
(FT_VCF . 2))))
(lambda (k) (assq-ref sym-tab k))))
(export ffi-htslib-symbol-val)
(define (unwrap-enum obj)
(cond ((number? obj) obj)
((symbol? obj) (ffi-htslib-symbol-val obj))
((fh-object? obj) (struct-ref obj 0))
(else (error "type mismatch"))))
(define ffi-htslib-types
'((pointer . "BGZF") "BGZF" (struct . "__kstring_t") (pointer . "kstring_t")
"kstring_t" (struct . "htsFormat") (pointer . "htsFormat") "htsFormat"
(pointer . "htsFile") "htsFile" (pointer . "htsThreadPool")
"htsThreadPool" (struct . "hts_opt") (pointer . "hts_opt") "hts_opt"
(pointer . "hts_idx_t") "hts_idx_t" (pointer . "hts_pair64_t")
"hts_pair64_t" (pointer . "hts_itr_t") "hts_itr_t" "hts_name2id_f"
"hts_id2name_f" (pointer . "errmod_t") "errmod_t" (struct .
"probaln_par_t") (pointer . "probaln_par_t") "probaln_par_t" (pointer .
"hts_md5_context") "hts_md5_context"))
(export ffi-htslib-types)
;; TODO: add renamer
;; --- last line ---
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