Sure, I will upload the patches. I am currently working on adapting the changes to the latest upstream version.
Also I have added a minor change to patch '02-fix-alignment.patch', which you will find attached. Best Regards Aleksandar Zlicic
Index: htslib-0.2.0~rc3/sam.c =================================================================== --- htslib-0.2.0~rc3.orig/sam.c +++ htslib-0.2.0~rc3/sam.c @@ -7,6 +7,7 @@ #include "htslib/sam.h" #include "htslib/bgzf.h" #include "cram/cram.h" +#include "cram/os.h" #include "hfile.h" #include "htslib/khash.h" @@ -726,18 +727,69 @@ int sam_format1(const bam_hdr_t *h, cons s = bam_get_aux(b); // aux while (s < b->data + b->l_data) { uint8_t type, key[2]; + uint8_t tmpData[8]; + int j; key[0] = s[0]; key[1] = s[1]; s += 2; type = *s++; kputc('\t', str); kputsn((char*)key, 2, str); kputc(':', str); if (type == 'A') { kputsn("A:", 2, str); kputc(*s, str); ++s; } else if (type == 'C') { kputsn("i:", 2, str); kputw(*s, str); ++s; } else if (type == 'c') { kputsn("i:", 2, str); kputw(*(int8_t*)s, str); ++s; } +#ifdef ALLOW_UAC else if (type == 'S') { kputsn("i:", 2, str); kputw(*(uint16_t*)s, str); s += 2; } else if (type == 's') { kputsn("i:", 2, str); kputw(*(int16_t*)s, str); s += 2; } else if (type == 'I') { kputsn("i:", 2, str); kputuw(*(uint32_t*)s, str); s += 4; } else if (type == 'i') { kputsn("i:", 2, str); kputw(*(int32_t*)s, str); s += 4; } else if (type == 'f') { ksprintf(str, "f:%g", *(float*)s); s += 4; } else if (type == 'd') { ksprintf(str, "d:%g", *(double*)s); s += 8; } +#else + else if (type == 'S') + { + uint16_t *ptmpData = (uint16_t*)&tmpData; + for(j=0;j<2;j++) tmpData[j]=s[j]; + kputsn("i:", 2, str); + kputw(*ptmpData, str); + s += 2; + } + else if (type == 's') + { + int16_t *ptmpData = (int16_t*)&tmpData; + for(j=0;j<2;j++) tmpData[j]=s[j]; + kputsn("i:", 2, str); + kputw(*ptmpData, str); + s += 2; + } + else if (type == 'I') + { + uint32_t *ptmpData = (uint32_t*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=s[j]; + kputsn("i:", 2, str); + kputuw(*ptmpData, str); + s += 4; + } + else if (type == 'i') + { + int32_t *ptmpData = (int32_t*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=s[j]; + kputsn("i:", 2, str); + kputw(*ptmpData, str); + s += 4; + } + else if (type == 'f') + { + float *ptmpData = (float*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=s[j]; + ksprintf(str, "f:%g", *ptmpData); + s += 4; + } + else if (type == 'd') + { + float *ptmpData = (float*)&tmpData; + for(j=0;j<8;j++) tmpData[j]=s[j]; + ksprintf(str, "d:%g", *ptmpData); + s += 8; + } +#endif else if (type == 'Z' || type == 'H') { kputc(type, str); kputc(':', str); while (*s) kputc(*s++, str); ++s; } else if (type == 'B') { uint8_t sub_type = *(s++); @@ -749,11 +801,49 @@ int sam_format1(const bam_hdr_t *h, cons kputc(',', str); if ('c' == sub_type) { kputw(*(int8_t*)s, str); ++s; } else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; } +#ifdef ALLOW_UAC else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; } else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; } else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; } else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; } else if ('f' == sub_type) { ksprintf(str, "%g", *(float*)s); s += 4; } +#else + else if ('s' == sub_type) + { + int16_t *ptmpData = (int16_t*)&tmpData; + for(j=0;j<2;j++) tmpData[j]=s[j]; + kputw(*ptmpData, str); + s += 2; + } + else if ('S' == sub_type) + { + uint16_t *ptmpData = (uint16_t*)&tmpData; + for(j=0;j<2;j++) tmpData[j]=s[j]; + kputw(*ptmpData, str); + s += 2; + } + else if ('i' == sub_type) + { + int32_t *ptmpData = (int32_t*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=s[j]; + kputw(*ptmpData, str); + s += 4; + } + else if ('I' == sub_type) + { + uint32_t *ptmpData = (uint32_t *)&tmpData; + for(j=0;j<4;j++) tmpData[j]=s[j]; + kputuw(*ptmpData, str); + s += 4; + } + else if ('f' == sub_type) + { + float *ptmpData = (float*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=s[j]; + ksprintf(str, "%g", *ptmpData); + s += 4; + } +#endif } } } @@ -838,11 +928,21 @@ int32_t bam_aux2i(const uint8_t *s) { int type; type = *s++; +#ifdef ALLOW_UAC if (type == 'c') return (int32_t)*(int8_t*)s; else if (type == 'C') return (int32_t)*(uint8_t*)s; else if (type == 's') return (int32_t)*(int16_t*)s; else if (type == 'S') return (int32_t)*(uint16_t*)s; else if (type == 'i' || type == 'I') return *(int32_t*)s; +#else + uint8_t tmpData[4]; + int j; + if (type == 'c') return (int32_t)*(int8_t*)s; + else if (type == 'C') return (int32_t)*(uint8_t*)s; + else if (type == 's'){ int16_t *ptmpData = (int16_t*)&tmpData; for(j=0;j<2;j++)tmpData[j]=s[j]; return (int32_t)(*ptmpData);} + else if (type == 'S'){ uint16_t *ptmpData = (uint16_t*)&tmpData; for(j=0;j<2;j++)tmpData[j]=s[j]; return (int32_t)*ptmpData;} + else if (type == 'i' || type == 'I'){ int32_t *ptmpData = (int32_t*)&tmpData; for(j=0;j<4;j++)tmpData[j]=s[j]; return *ptmpData;} +#endif else return 0; } @@ -850,8 +950,25 @@ double bam_aux2f(const uint8_t *s) { int type; type = *s++; +#ifdef ALLOW_UAC if (type == 'd') return *(double*)s; else if (type == 'f') return *(float*)s; +#else + uint8_t tmpData[8]; + int j; + if (type == 'd') + { + double *ptmpData = (double*)&tmpData; + for(j=0;j<sizeof(double);j++) tmpData[j]=s[j]; + return *ptmpData; + } + else if (type == 'f') + { + float *ptmpData = (float*)&tmpData; + for(j=0;j<sizeof(float);j++) tmpData[j]=s[j]; + return *ptmpData; + } +#endif else return 0.0; } Index: htslib-0.2.0~rc3/vcf.c =================================================================== --- htslib-0.2.0~rc3.orig/vcf.c +++ htslib-0.2.0~rc3/vcf.c @@ -10,6 +10,7 @@ #include "htslib/vcf.h" #include "htslib/tbx.h" #include "hfile.h" +#include "cram/os.h" #include "htslib/khash.h" KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) @@ -1435,6 +1436,10 @@ static inline uint8_t *bcf_unpack_fmt_co static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info) { uint8_t *ptr_start = ptr; +#ifndef ALLOW_UAC + uint8_t tmpData[4]; + int j; +#endif info->key = bcf_dec_typed_int1(ptr, &ptr); info->len = bcf_dec_size(ptr, &ptr, &info->type); info->vptr = ptr; @@ -1443,9 +1448,30 @@ static inline uint8_t *bcf_unpack_info_c info->v1.i = 0; if (info->len == 1) { if (info->type == BCF_BT_INT8 || info->type == BCF_BT_CHAR) info->v1.i = *(int8_t*)ptr; +#ifdef ALLOW_UAC else if (info->type == BCF_BT_INT32) info->v1.i = *(int32_t*)ptr; else if (info->type == BCF_BT_FLOAT) info->v1.f = *(float*)ptr; else if (info->type == BCF_BT_INT16) info->v1.i = *(int16_t*)ptr; +#else + else if (info->type == BCF_BT_INT32) + { + int32_t *ptmpData = (int32_t*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=ptr[j]; + info->v1.i = *ptmpData; + } + else if (info->type == BCF_BT_FLOAT) + { + float *ptmpData = (float*)&tmpData; + for(j=0;j<4;j++) tmpData[j]=ptr[j]; + info->v1.f = *ptmpData; + } + else if (info->type == BCF_BT_INT16) + { + int16_t *ptmpData = (int16_t*)&tmpData; + for(j=0;j<2;j++) tmpData[j]=ptr[j]; + info->v1.i = *ptmpData; + } +#endif } ptr += info->len << bcf_type_shift[info->type]; info->vptr_len = ptr - info->vptr; Index: htslib-0.2.0~rc3/htslib/hts.h =================================================================== --- htslib-0.2.0~rc3.orig/htslib/hts.h +++ htslib-0.2.0~rc3/htslib/hts.h @@ -238,7 +238,17 @@ static inline uint16_t ed_swap_2(uint16_ } static inline void *ed_swap_2p(void *x) { +#ifdef ALLOW_UAC *(uint16_t*)x = ed_swap_2(*(uint16_t*)x); +#else + uint8_t tmpData[2]; + uint16_t *ptmpData = (uint16_t*)&tmpData; + uint8_t *px = (uint8_t*)x; + int j; + for(j=0;j<2;j++) tmpData[j] = px[j]; + *ptmpData = ed_swap_2(*ptmpData); + for(j=0;j<2;j++) px[j] = tmpData[j]; +#endif return x; } static inline uint32_t ed_swap_4(uint32_t v) @@ -248,7 +258,17 @@ static inline uint32_t ed_swap_4(uint32_ } static inline void *ed_swap_4p(void *x) { +#ifdef ALLOW_UAC *(uint32_t*)x = ed_swap_4(*(uint32_t*)x); +#else + uint8_t tmpData[4]; + uint32_t *ptmpData = (uint32_t*)&tmpData; + uint8_t *px = (uint8_t*)x; + int j; + for(j=0;j<4;j++) tmpData[j] = px[j]; + *ptmpData = ed_swap_4(*ptmpData); + for(j=0;j<4;j++) px[j] = tmpData[j]; +#endif return x; } static inline uint64_t ed_swap_8(uint64_t v) @@ -259,7 +279,17 @@ static inline uint64_t ed_swap_8(uint64_ } static inline void *ed_swap_8p(void *x) { +#ifdef ALLOW_UAC *(uint64_t*)x = ed_swap_8(*(uint64_t*)x); +#else + uint8_t tmpData[8]; + uint64_t *ptmpData = (uint64_t*)&tmpData; + uint8_t *px = (uint8_t*)x; + int j; + for(j=0;j<8;j++) tmpData[j] = px[j]; + *ptmpData = ed_swap_8(*ptmpData); + for(j=0;j<8;j++) px[j] = tmpData[j]; +#endif return x; }