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// This library is part of PLINK 2.0, copyright (C) 2005-2025 Shaun Purcell,
// Christopher Chang.
//
// This library is free software: you can redistribute it and/or modify it
// under the terms of the GNU Lesser General Public License as published by the
// Free Software Foundation, either version 3 of the License, or (at your
// option) any later version.
//
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
// for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library. If not, see <http://www.gnu.org/licenses/>.
#include <errno.h>
#include "plink2_compress_stream.h"
#ifdef __cplusplus
namespace plink2 {
#endif
uint32_t g_zst_level = 0;
PglErr InitCstreamNoop(const char* out_fname, uint32_t do_append, char* overflow_buf, CompressStreamState* css_ptr) {
// css_ptr->z_outfile = nullptr;
css_ptr->cctx = nullptr;
// can't use fopen_checked since we need to be able to append
css_ptr->outfile = fopen(out_fname, do_append? FOPEN_AB : FOPEN_WB);
if (unlikely(!css_ptr->outfile)) {
logputs("\n");
logerrprintfww(kErrprintfFopen, out_fname, strerror(errno));
return kPglRetOpenFail;
}
css_ptr->overflow_buf = overflow_buf;
return kPglRetSuccess;
}
PglErr InitCstreamZstd(const char* out_fname, uint32_t do_append, __maybe_unused uint32_t thread_ct, uintptr_t overflow_buf_size, char* overflow_buf, unsigned char* compress_wkspace, CompressStreamState* css_ptr) {
css_ptr->outfile = nullptr;
css_ptr->cctx = ZSTD_createCCtx();
if (unlikely(!css_ptr->cctx)) {
return kPglRetNomem;
}
__maybe_unused size_t retval = ZSTD_CCtx_setParameter(css_ptr->cctx, ZSTD_c_compressionLevel, g_zst_level);
assert(!ZSTD_isError(retval));
#ifdef ZSTD_MULTITHREAD
// ignore failure; if zstd is dynamically linked and was built without MT
// support, so be it
ZSTD_CCtx_setParameter(css_ptr->cctx, ZSTD_c_nbWorkers, thread_ct);
#endif
css_ptr->outfile = fopen(out_fname, do_append? FOPEN_AB : FOPEN_WB);
if (unlikely(!css_ptr->outfile)) {
logputs("\n");
logerrprintfww(kErrprintfFopen, out_fname, strerror(errno));
ZSTD_freeCCtx(css_ptr->cctx); // might return an error later?
return kPglRetOpenFail;
}
css_ptr->output.dst = compress_wkspace;
css_ptr->output.size = CstreamWkspaceReq(overflow_buf_size);
css_ptr->output.pos = 0;
css_ptr->overflow_buf = overflow_buf;
return kPglRetSuccess;
}
// possible todo: replace output_zst with an enum which permits gzipping
PglErr InitCstream(const char* out_fname, uint32_t do_append, uint32_t output_zst, uint32_t thread_ct, uintptr_t overflow_buf_size, char* overflow_buf, unsigned char* compress_wkspace, CompressStreamState* css_ptr) {
if (!output_zst) {
return InitCstreamNoop(out_fname, do_append, overflow_buf, css_ptr);
}
return InitCstreamZstd(out_fname, do_append, thread_ct, overflow_buf_size, overflow_buf, compress_wkspace, css_ptr);
}
PglErr InitCstreamAlloc(const char* out_fname, uint32_t do_append, uint32_t output_zst, uint32_t thread_ct, uintptr_t overflow_buf_size, CompressStreamState* css_ptr, char** cswritepp) {
char* overflow_buf;
if (unlikely(bigstack_alloc_c(overflow_buf_size, &overflow_buf))) {
return kPglRetNomem;
}
unsigned char* compress_wkspace = nullptr;
if (output_zst) {
if (unlikely(bigstack_alloc_uc(CstreamWkspaceReq(overflow_buf_size), &compress_wkspace))) {
return kPglRetNomem;
}
}
PglErr reterr = InitCstream(out_fname, do_append, output_zst, thread_ct, overflow_buf_size, overflow_buf, compress_wkspace, css_ptr);
*cswritepp = overflow_buf;
return reterr;
}
BoolErr ForceUncompressedCswrite(CompressStreamState* css_ptr, char** writep_ptr) {
char* writep = *writep_ptr;
if (css_ptr->overflow_buf != writep) {
if (unlikely(fwrite_checked(css_ptr->overflow_buf, writep - css_ptr->overflow_buf, css_ptr->outfile))) {
return 1;
}
*writep_ptr = css_ptr->overflow_buf;
}
return 0;
}
BoolErr ForceCompressedCswrite(CompressStreamState* css_ptr, char** writep_ptr) {
char* overflow_buf = css_ptr->overflow_buf;
char* writep = *writep_ptr;
if (overflow_buf != writep) {
const uintptr_t in_size = writep - overflow_buf;
ZSTD_inBuffer input = {overflow_buf, in_size, 0};
while (1) {
// todo: conditionally support seekable files
__maybe_unused size_t retval = ZSTD_compressStream2(css_ptr->cctx, &css_ptr->output, &input, ZSTD_e_continue);
assert(!ZSTD_isError(retval));
if (css_ptr->output.pos >= kCompressStreamBlock) {
if (unlikely(fwrite_checked(css_ptr->output.dst, css_ptr->output.pos, css_ptr->outfile))) {
return 1;
}
css_ptr->output.pos = 0;
}
const uintptr_t bytes_left = input.size - input.pos;
if (bytes_left < kCompressStreamBlock) {
memmove(overflow_buf, &(overflow_buf[in_size - bytes_left]), bytes_left);
*writep_ptr = &(overflow_buf[bytes_left]);
break;
}
}
}
return 0;
}
BoolErr CsputsStd(const char* readp, uint32_t byte_ct, CompressStreamState* css_ptr, char** writep_ptr) {
char* writep = *writep_ptr;
char* overflow_buf = css_ptr->overflow_buf;
uint32_t cur_write_space = 2 * kCompressStreamBlock - S_CAST(uintptr_t, writep - overflow_buf);
if (IsUncompressedCstream(css_ptr)) {
while (byte_ct > cur_write_space) {
memcpy(writep, readp, cur_write_space);
if (unlikely(!fwrite_unlocked(overflow_buf, 2 * kCompressStreamBlock, 1, css_ptr->outfile))) {
return 1;
}
writep = overflow_buf;
readp = &(readp[cur_write_space]);
byte_ct -= cur_write_space;
cur_write_space = 2 * kCompressStreamBlock;
}
} else {
while (byte_ct > cur_write_space) {
memcpy(writep, readp, cur_write_space);
ZSTD_inBuffer input = {overflow_buf, 2 * kCompressStreamBlock, 0};
while (1) {
// todo: conditionally support seekable files
__maybe_unused size_t retval = ZSTD_compressStream2(css_ptr->cctx, &css_ptr->output, &input, ZSTD_e_continue);
assert(!ZSTD_isError(retval));
if (css_ptr->output.pos >= kCompressStreamBlock) {
if (unlikely(!fwrite_unlocked(css_ptr->output.dst, css_ptr->output.pos, 1, css_ptr->outfile))) {
return 1;
}
css_ptr->output.pos = 0;
}
const uintptr_t bytes_left = input.size - input.pos;
if (bytes_left < kCompressStreamBlock) {
memmove(overflow_buf, &(overflow_buf[2 * kCompressStreamBlock - bytes_left]), bytes_left);
writep = &(overflow_buf[retval]);
break;
}
}
readp = &(readp[cur_write_space]);
byte_ct -= cur_write_space;
cur_write_space = 2 * kCompressStreamBlock - S_CAST(uintptr_t, writep - overflow_buf);
}
}
memcpy(writep, readp, byte_ct);
*writep_ptr = &(writep[byte_ct]);
return Cswrite(css_ptr, writep_ptr);
}
BoolErr UncompressedCswriteCloseNull(CompressStreamState* css_ptr, char* writep) {
ForceUncompressedCswrite(css_ptr, &writep);
css_ptr->overflow_buf = nullptr;
int32_t ii = ferror_unlocked(css_ptr->outfile);
int32_t jj = fclose(css_ptr->outfile);
return ii || jj;
}
BoolErr CompressedCswriteCloseNull(CompressStreamState* css_ptr, char* writep) {
char* overflow_buf = css_ptr->overflow_buf;
const uintptr_t in_size = writep - overflow_buf;
ZSTD_inBuffer input = {overflow_buf, in_size, 0};
BoolErr reterr = 0;
while (1) {
__maybe_unused size_t retval = ZSTD_compressStream2(css_ptr->cctx, &css_ptr->output, &input, ZSTD_e_end);
assert(!ZSTD_isError(retval));
if (css_ptr->output.pos) {
if (unlikely(fwrite_checked(css_ptr->output.dst, css_ptr->output.pos, css_ptr->outfile))) {
reterr = 1;
}
css_ptr->output.pos = 0;
}
if (!retval) {
break;
}
}
ZSTD_freeCCtx(css_ptr->cctx); // might return an error later?
css_ptr->overflow_buf = nullptr;
int32_t ii = ferror_unlocked(css_ptr->outfile);
int32_t jj = fclose(css_ptr->outfile);
return reterr || ii || jj;
}
BoolErr CswriteCloseNull(CompressStreamState* css_ptr, char* writep) {
if (IsUncompressedCstream(css_ptr)) {
return UncompressedCswriteCloseNull(css_ptr, writep);
}
return CompressedCswriteCloseNull(css_ptr, writep);
}
#ifdef __cplusplus
}
#endif
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