/*
 * This file was generated automatically by ExtUtils::ParseXS version 3.51 from the
 * contents of FASTX.xs. Do not edit this file, edit FASTX.xs instead.
 *
 *    ANY CHANGES MADE HERE WILL BE LOST!
 *
 */

#line 1 "FASTX.xs"
/* FASTA/FASTQ parser using kseq.h */
#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"

#include <zlib.h>
#include "kseq.h"

// Initialize kseq
KSEQ_INIT(gzFile, gzread)

// Helper function to convert a kseq_t record to a Perl hash reference
static SV* kseq_to_hash(pTHX_ kseq_t *seq) {
    HV* hash = newHV();
    
    // Add name, always present
    hv_store(hash, "name", 4, newSVpvn(seq->name.s, seq->name.l), 0);
    
    // Add sequence, always present
    hv_store(hash, "seq", 3, newSVpvn(seq->seq.s, seq->seq.l), 0);
    
    // Add comment if present
    if (seq->comment.l)
        hv_store(hash, "comment", 7, newSVpvn(seq->comment.s, seq->comment.l), 0);
    
    // Add quality if present
    if (seq->qual.l)
        hv_store(hash, "qual", 4, newSVpvn(seq->qual.s, seq->qual.l), 0);
    
    return newRV_noinc((SV*)hash);
}

#line 43 "FASTX.c"
#ifndef PERL_UNUSED_VAR
#  define PERL_UNUSED_VAR(var) if (0) var = var
#endif

#ifndef dVAR
#  define dVAR		dNOOP
#endif


/* This stuff is not part of the API! You have been warned. */
#ifndef PERL_VERSION_DECIMAL
#  define PERL_VERSION_DECIMAL(r,v,s) (r*1000000 + v*1000 + s)
#endif
#ifndef PERL_DECIMAL_VERSION
#  define PERL_DECIMAL_VERSION \
	  PERL_VERSION_DECIMAL(PERL_REVISION,PERL_VERSION,PERL_SUBVERSION)
#endif
#ifndef PERL_VERSION_GE
#  define PERL_VERSION_GE(r,v,s) \
	  (PERL_DECIMAL_VERSION >= PERL_VERSION_DECIMAL(r,v,s))
#endif
#ifndef PERL_VERSION_LE
#  define PERL_VERSION_LE(r,v,s) \
	  (PERL_DECIMAL_VERSION <= PERL_VERSION_DECIMAL(r,v,s))
#endif

/* XS_INTERNAL is the explicit static-linkage variant of the default
 * XS macro.
 *
 * XS_EXTERNAL is the same as XS_INTERNAL except it does not include
 * "STATIC", ie. it exports XSUB symbols. You probably don't want that
 * for anything but the BOOT XSUB.
 *
 * See XSUB.h in core!
 */


/* TODO: This might be compatible further back than 5.10.0. */
#if PERL_VERSION_GE(5, 10, 0) && PERL_VERSION_LE(5, 15, 1)
#  undef XS_EXTERNAL
#  undef XS_INTERNAL
#  if defined(__CYGWIN__) && defined(USE_DYNAMIC_LOADING)
#    define XS_EXTERNAL(name) __declspec(dllexport) XSPROTO(name)
#    define XS_INTERNAL(name) STATIC XSPROTO(name)
#  endif
#  if defined(__SYMBIAN32__)
#    define XS_EXTERNAL(name) EXPORT_C XSPROTO(name)
#    define XS_INTERNAL(name) EXPORT_C STATIC XSPROTO(name)
#  endif
#  ifndef XS_EXTERNAL
#    if defined(HASATTRIBUTE_UNUSED) && !defined(__cplusplus)
#      define XS_EXTERNAL(name) void name(pTHX_ CV* cv __attribute__unused__)
#      define XS_INTERNAL(name) STATIC void name(pTHX_ CV* cv __attribute__unused__)
#    else
#      ifdef __cplusplus
#        define XS_EXTERNAL(name) extern "C" XSPROTO(name)
#        define XS_INTERNAL(name) static XSPROTO(name)
#      else
#        define XS_EXTERNAL(name) XSPROTO(name)
#        define XS_INTERNAL(name) STATIC XSPROTO(name)
#      endif
#    endif
#  endif
#endif

/* perl >= 5.10.0 && perl <= 5.15.1 */


/* The XS_EXTERNAL macro is used for functions that must not be static
 * like the boot XSUB of a module. If perl didn't have an XS_EXTERNAL
 * macro defined, the best we can do is assume XS is the same.
 * Dito for XS_INTERNAL.
 */
#ifndef XS_EXTERNAL
#  define XS_EXTERNAL(name) XS(name)
#endif
#ifndef XS_INTERNAL
#  define XS_INTERNAL(name) XS(name)
#endif

/* Now, finally, after all this mess, we want an ExtUtils::ParseXS
 * internal macro that we're free to redefine for varying linkage due
 * to the EXPORT_XSUB_SYMBOLS XS keyword. This is internal, use
 * XS_EXTERNAL(name) or XS_INTERNAL(name) in your code if you need to!
 */

#undef XS_EUPXS
#if defined(PERL_EUPXS_ALWAYS_EXPORT)
#  define XS_EUPXS(name) XS_EXTERNAL(name)
#else
   /* default to internal */
#  define XS_EUPXS(name) XS_INTERNAL(name)
#endif

#ifndef PERL_ARGS_ASSERT_CROAK_XS_USAGE
#define PERL_ARGS_ASSERT_CROAK_XS_USAGE assert(cv); assert(params)

/* prototype to pass -Wmissing-prototypes */
STATIC void
S_croak_xs_usage(const CV *const cv, const char *const params);

STATIC void
S_croak_xs_usage(const CV *const cv, const char *const params)
{
    const GV *const gv = CvGV(cv);

    PERL_ARGS_ASSERT_CROAK_XS_USAGE;

    if (gv) {
        const char *const gvname = GvNAME(gv);
        const HV *const stash = GvSTASH(gv);
        const char *const hvname = stash ? HvNAME(stash) : NULL;

        if (hvname)
	    Perl_croak_nocontext("Usage: %s::%s(%s)", hvname, gvname, params);
        else
	    Perl_croak_nocontext("Usage: %s(%s)", gvname, params);
    } else {
        /* Pants. I don't think that it should be possible to get here. */
	Perl_croak_nocontext("Usage: CODE(0x%" UVxf ")(%s)", PTR2UV(cv), params);
    }
}
#undef  PERL_ARGS_ASSERT_CROAK_XS_USAGE

#define croak_xs_usage        S_croak_xs_usage

#endif

/* NOTE: the prototype of newXSproto() is different in versions of perls,
 * so we define a portable version of newXSproto()
 */
#ifdef newXS_flags
#define newXSproto_portable(name, c_impl, file, proto) newXS_flags(name, c_impl, file, proto, 0)
#else
#define newXSproto_portable(name, c_impl, file, proto) (PL_Sv=(SV*)newXS(name, c_impl, file), sv_setpv(PL_Sv, proto), (CV*)PL_Sv)
#endif /* !defined(newXS_flags) */

#if PERL_VERSION_LE(5, 21, 5)
#  define newXS_deffile(a,b) Perl_newXS(aTHX_ a,b,file)
#else
#  define newXS_deffile(a,b) Perl_newXS_deffile(aTHX_ a,b)
#endif

#line 187 "FASTX.c"

XS_EUPXS(XS_FASTX__XS__xs_new); /* prototype to pass -Wmissing-prototypes */
XS_EUPXS(XS_FASTX__XS__xs_new)
{
    dVAR; dXSARGS;
    if (items != 2)
       croak_xs_usage(cv,  "class, filename");
    {
	char*	class = (char *)SvPV_nolen(ST(0))
;
	char*	filename = (char *)SvPV_nolen(ST(1))
;
	SV *	RETVAL;
#line 41 "FASTX.xs"
        gzFile fp;
        kseq_t *seq;

        // Open the file
        fp = gzopen(filename, "r");
        if (fp == NULL)
            croak("Failed to open file: %s", filename);

        // Initialize kseq
        seq = kseq_init(fp);

        // Create a hash to store our object data
        HV* self = newHV();

        // Store the file pointer and seq object as an IV
        hv_store(self, "_fp", 3, newSViv(PTR2IV(fp)), 0);
        hv_store(self, "_seq", 4, newSViv(PTR2IV(seq)), 0);

        // Bless and return
        RETVAL = sv_bless(newRV_noinc((SV*)self), gv_stashpv(class, 0));
#line 222 "FASTX.c"
	RETVAL = sv_2mortal(RETVAL);
	ST(0) = RETVAL;
    }
    XSRETURN(1);
}


XS_EUPXS(XS_FASTX__XS_next_seq); /* prototype to pass -Wmissing-prototypes */
XS_EUPXS(XS_FASTX__XS_next_seq)
{
    dVAR; dXSARGS;
    if (items != 1)
       croak_xs_usage(cv,  "self");
    {
	SV*	self = ST(0)
;
	SV *	RETVAL;
#line 68 "FASTX.xs"
        HV* hash;
        SV** fp_sv;
        SV** seq_sv;
        gzFile fp;
        kseq_t *seq;
        int ret;

        // Get the hash
        if (!SvROK(self) || SvTYPE(SvRV(self)) != SVt_PVHV)
            croak("Not a blessed hash reference");
        hash = (HV*)SvRV(self);

        // Get the file pointer and seq object
        fp_sv = hv_fetch(hash, "_fp", 3, 0);
        seq_sv = hv_fetch(hash, "_seq", 4, 0);

        if (!fp_sv || !seq_sv)
            croak("Invalid object");

        fp = INT2PTR(gzFile, SvIV(*fp_sv));
        seq = INT2PTR(kseq_t*, SvIV(*seq_sv));

        // Read next sequence
        ret = kseq_read(seq);

        if (ret < 0) {
            // EOF or error
            RETVAL = &PL_sv_undef;
        } else {
            // Convert to hash and return
            RETVAL = kseq_to_hash(aTHX_ seq);
        }
#line 273 "FASTX.c"
	RETVAL = sv_2mortal(RETVAL);
	ST(0) = RETVAL;
    }
    XSRETURN(1);
}


XS_EUPXS(XS_FASTX__XS_DESTROY); /* prototype to pass -Wmissing-prototypes */
XS_EUPXS(XS_FASTX__XS_DESTROY)
{
    dVAR; dXSARGS;
    if (items != 1)
       croak_xs_usage(cv,  "self");
    {
	SV*	self = ST(0)
;
#line 107 "FASTX.xs"
        HV* hash;
        SV** fp_sv;
        SV** seq_sv;
        gzFile fp;
        kseq_t *seq;

        // Get the hash
        if (!SvROK(self) || SvTYPE(SvRV(self)) != SVt_PVHV)
            return;
        hash = (HV*)SvRV(self);

        // Get the file pointer and seq object
        fp_sv = hv_fetch(hash, "_fp", 3, 0);
        seq_sv = hv_fetch(hash, "_seq", 4, 0);

        if (!fp_sv || !seq_sv)
            return;

        fp = INT2PTR(gzFile, SvIV(*fp_sv));
        seq = INT2PTR(kseq_t*, SvIV(*seq_sv));

        // Clean up
        kseq_destroy(seq);
        gzclose(fp);
#line 315 "FASTX.c"
    }
    XSRETURN_EMPTY;
}

#ifdef __cplusplus
extern "C" {
#endif
XS_EXTERNAL(boot_FASTX__XS); /* prototype to pass -Wmissing-prototypes */
XS_EXTERNAL(boot_FASTX__XS)
{
#if PERL_VERSION_LE(5, 21, 5)
    dVAR; dXSARGS;
#else
    dVAR; dXSBOOTARGSXSAPIVERCHK;
#endif
#if PERL_VERSION_LE(5, 8, 999) /* PERL_VERSION_LT is 5.33+ */
    char* file = __FILE__;
#else
    const char* file = __FILE__;
#endif

    PERL_UNUSED_VAR(file);

    PERL_UNUSED_VAR(cv); /* -W */
    PERL_UNUSED_VAR(items); /* -W */
#if PERL_VERSION_LE(5, 21, 5)
    XS_VERSION_BOOTCHECK;
#  ifdef XS_APIVERSION_BOOTCHECK
    XS_APIVERSION_BOOTCHECK;
#  endif
#endif

        newXS_deffile("FASTX::XS::_xs_new", XS_FASTX__XS__xs_new);
        newXS_deffile("FASTX::XS::next_seq", XS_FASTX__XS_next_seq);
        newXS_deffile("FASTX::XS::DESTROY", XS_FASTX__XS_DESTROY);
#if PERL_VERSION_LE(5, 21, 5)
#  if PERL_VERSION_GE(5, 9, 0)
    if (PL_unitcheckav)
        call_list(PL_scopestack_ix, PL_unitcheckav);
#  endif
    XSRETURN_YES;
#else
    Perl_xs_boot_epilog(aTHX_ ax);
#endif
}

#ifdef __cplusplus
}
#endif
