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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| # Makefile for htslib, a C library for high-throughput sequencing data formats. | ||
| # | ||
| # Copyright (C) 2013-2021 Genome Research Ltd. | ||
| # Copyright (C) 2013-2022 Genome Research Ltd. | ||
| # | ||
| # Author: John Marshall <[email protected]> | ||
| # | ||
|
|
@@ -131,8 +131,8 @@ LIBHTS_SOVERSION = 3 | |
| # is not strictly necessary and should be removed the next time | ||
| # LIBHTS_SOVERSION is bumped (see #1144 and | ||
| # https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23) | ||
| MACH_O_COMPATIBILITY_VERSION = 3.1.14 | ||
| MACH_O_CURRENT_VERSION = 3.1.14 | ||
| MACH_O_COMPATIBILITY_VERSION = 3.1.15 | ||
| MACH_O_CURRENT_VERSION = 3.1.15 | ||
|
|
||
| # $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string | ||
| # even if this is a dirty or untagged Git working tree. | ||
|
|
@@ -282,10 +282,10 @@ SHLIB_FLAVOUR = cygdll | |
| lib-shared: cyghts-$(LIBHTS_SOVERSION).dll | ||
| else ifeq "$(findstring MSYS,$(PLATFORM))" "MSYS" | ||
| SHLIB_FLAVOUR = dll | ||
| lib-shared: hts-$(LIBHTS_SOVERSION).dll | ||
| lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib | ||
| else ifeq "$(findstring MINGW,$(PLATFORM))" "MINGW" | ||
| SHLIB_FLAVOUR = dll | ||
| lib-shared: hts-$(LIBHTS_SOVERSION).dll | ||
| lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib | ||
| else | ||
| SHLIB_FLAVOUR = so | ||
| lib-shared: libhts.so | ||
|
|
@@ -330,6 +330,41 @@ cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS) | |
| hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS) | ||
| $(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread | ||
|
|
||
| hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll | ||
| gendef hts-$(LIBHTS_SOVERSION).dll | ||
|
|
||
| hts-$(LIBHTS_SOVERSION).lib: hts-$(LIBHTS_SOVERSION).def | ||
| dlltool -m i386:x86-64 -d hts-$(LIBHTS_SOVERSION).def -l hts-$(LIBHTS_SOVERSION).lib | ||
|
|
||
| # Bundling libraries, binaries, dll dependencies, and licenses into a | ||
| # single directory. NB: This is not needed for end-users, but a test bed | ||
| # for maintainers building binary distributions. | ||
| # | ||
| # NOTE: only tested on the supported MSYS2/MINGW64 environment. | ||
| dist-windows: DESTDIR= | ||
| dist-windows: prefix=dist-windows | ||
| dist-windows: install | ||
| cp hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib dist-windows/lib | ||
| cp `ldd hts-$(LIBHTS_SOVERSION).dll| awk '/mingw64/ {print $$3}'` dist-windows/bin | ||
| mkdir -p dist-windows/share/licenses/htslib | ||
| -cp -r /mingw64/share/licenses/mingw-w64-libraries \ | ||
| /mingw64/share/licenses/brotli \ | ||
| /mingw64/share/licenses/bzip2 \ | ||
| /mingw64/share/licenses/gcc-libs \ | ||
| /mingw64/share/licenses/libdeflate \ | ||
| /mingw64/share/licenses/libpsl \ | ||
| /mingw64/share/licenses/libtre \ | ||
| /mingw64/share/licenses/libwinpthread \ | ||
| /mingw64/share/licenses/openssl \ | ||
| /mingw64/share/licenses/xz \ | ||
| /mingw64/share/licenses/zlib \ | ||
| /mingw64/share/licenses/zstd \ | ||
| dist-windows/share/licenses/ | ||
| -cp -r /usr/share/licenses/curl \ | ||
| dist-windows/share/licenses/ | ||
| cp LICENSE dist-windows/share/licenses/htslib/ | ||
|
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||
|
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||
| # Target to allow htslib.mk to build all the object files before it | ||
| # links the shared and static libraries. | ||
| hts-object-files: $(LIBHTS_OBJS) | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| /* | ||
| Copyright (c) 2012-2020 Genome Research Ltd. | ||
| Copyright (c) 2012-2020, 2022 Genome Research Ltd. | ||
| Author: James Bonfield <[email protected]> | ||
| Redistribution and use in source and binary forms, with or without | ||
|
|
@@ -1777,7 +1777,7 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s, | |
| } | ||
|
|
||
| cr->ncigar = ncigar - cr->cigar; | ||
| cr->aend = ref_pos; | ||
| cr->aend = ref_pos > cr->apos ? ref_pos : cr->apos; | ||
|
|
||
| //printf("2: %.*s %d .. %d\n", cr->name_len, DSTRING_STR(name_ds) + cr->name, cr->apos, ref_pos); | ||
|
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||
|
|
@@ -3228,15 +3228,17 @@ static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) { | |
| } | ||
|
|
||
| // position beyond end of range; bail out | ||
| if (c_next->ref_seq_start > fd->range.end) { | ||
| if (fd->range.refid != -1 && | ||
| c_next->ref_seq_start > fd->range.end) { | ||
| cram_free_container(c_next); | ||
| fd->ctr_mt = NULL; | ||
| fd->ooc = 1; | ||
| break; | ||
| } | ||
|
|
||
| // before start of range; skip to next container | ||
| if (c_next->ref_seq_start + c_next->ref_seq_span-1 < | ||
| if (fd->range.refid != -1 && | ||
| c_next->ref_seq_start + c_next->ref_seq_span-1 < | ||
| fd->range.start) { | ||
| c_next->curr_slice_mt = c_next->max_slice; | ||
| cram_seek(fd, c_next->length, SEEK_CUR); | ||
|
|
@@ -3301,15 +3303,17 @@ static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) { | |
| } | ||
|
|
||
| // position beyond end of range; bail out | ||
| if (s_next->hdr->ref_seq_start > fd->range.end) { | ||
| if (fd->range.refid != -1 && | ||
| s_next->hdr->ref_seq_start > fd->range.end) { | ||
| fd->ooc = 1; | ||
| cram_free_slice(s_next); | ||
| c_next->slice = s_next = NULL; | ||
| break; | ||
| } | ||
|
|
||
| // before start of range; skip to next slice | ||
| if (s_next->hdr->ref_seq_start + s_next->hdr->ref_seq_span-1 < | ||
| if (fd->range.refid != -1 && | ||
| s_next->hdr->ref_seq_start + s_next->hdr->ref_seq_span-1 < | ||
| fd->range.start) { | ||
| cram_free_slice(s_next); | ||
| c_next->slice = s_next = NULL; | ||
|
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||
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