Package: samtools Version: 0.1.19-1 Tags: sid patch Severity: important User: debian-mips-dev-disc...@lists.alioth.debian.org Usertags: mips-patch
'python-pysam' package FTBFS on mips/mipsel due to issues in 'samtools' package. Build log for 'python-pysam' on mips: https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mips&ver=0.7.7-1&stamp=1397894446 Build log for 'python-pysam' on mipsel: https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mipsel&ver=0.7.7-1&stamp=1397887877 Output of samtools executable from samtools package is used as a reference during tests in python-pysam (its output is compared with output from pysam python module), but samtools has both unaligned memory access and system endianness issues. I have attached patches that fix this. With these patches applied to samtools, python-pysam builds fine. Best Regards Aleksandar Zlicic
Index: samtools-0.1.19/bam_import.c =================================================================== --- samtools-0.1.19.orig/bam_import.c +++ samtools-0.1.19/bam_import.c @@ -21,6 +21,10 @@ void bam_init_header_hash(bam_header_t * void bam_destroy_header_hash(bam_header_t *header); int32_t bam_get_tid(const bam_header_t *header, const char *seq_name); +#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686) +# define ALLOW_UAC +#endif + unsigned char bam_nt16_table[256] = { 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, @@ -365,6 +369,10 @@ int sam_read1(tamFile fp, bam_header_t * if (dret != '\n' && dret != '\r') { // aux while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) { uint8_t *s, type, key[2]; +#ifndef ALLOW_UAC + uint8_t tmpData[8]; + int j; +#endif z += str->l + 1; if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':') parse_error(fp->n_lines, "missing colon in auxiliary data"); @@ -410,14 +418,30 @@ int sam_read1(tamFile fp, bam_header_t * } } } else if (type == 'f') { +#ifndef ALLOW_UAC + float *ptmpData = (float*)&tmpData; +#endif s = alloc_data(b, doff + 5) + doff; *s++ = 'f'; +#ifdef ALLOW_UAC *(float*)s = (float)atof(str->s + 5); +#else + *ptmpData = (float)atof(str->s + 5); + for(j=0;j<4;j++) s[j] = tmpData[j]; +#endif s += 4; doff += 5; } else if (type == 'd') { +#ifndef ALLOW_UAC + float *ptmpData = (float*)&tmpData; +#endif s = alloc_data(b, doff + 9) + doff; *s++ = 'd'; +#ifdef ALLOW_UAC *(float*)s = (float)atof(str->s + 9); +#else + *ptmpData = (float)atof(str->s + 9); + for(j=0;j<4;j++) s[j] = tmpData[j]; +#endif s += 8; doff += 9; } else if (type == 'Z' || type == 'H') { int size = 1 + (str->l - 5) + 1;
Index: samtools-0.1.19/bam.c =================================================================== --- samtools-0.1.19.orig/bam.c +++ samtools-0.1.19/bam.c @@ -157,7 +157,7 @@ int bam_header_write(bamFile fp, const b return 0; } -static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data) +static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data, int is_host) { uint8_t *s; uint32_t i, *cigar = (uint32_t*)(data + c->l_qname); @@ -174,16 +174,18 @@ static void swap_endian_data(const bam1_ else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; } else if (type == 'B') { int32_t n, Bsize = bam_aux_type2size(*s); + if(!is_host) bam_swap_endian_4p(s+1); memcpy(&n, s + 1, 4); if (1 == Bsize) { } else if (2 == Bsize) { - for (i = 0; i < n; i += 2) + for (i = 0; i < n*Bsize; i += 2) bam_swap_endian_2p(s + 5 + i); } else if (4 == Bsize) { - for (i = 0; i < n; i += 4) + for (i = 0; i < n*Bsize; i += 4) bam_swap_endian_4p(s + 5 + i); } - bam_swap_endian_4p(s+1); + if(is_host) bam_swap_endian_4p(s+1); + s += n * Bsize + 4; } } } @@ -217,7 +219,7 @@ int bam_read1(bamFile fp, bam1_t *b) } if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4; b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2; - if (bam_is_be) swap_endian_data(c, b->data_len, b->data); + if (bam_is_be) swap_endian_data(c, b->data_len, b->data, 0); if (bam_no_B) bam_remove_B(b); return 4 + block_len; } @@ -240,11 +242,11 @@ inline int bam_write1_core(bamFile fp, c for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i); y = block_len; bam_write(fp, bam_swap_endian_4p(&y), 4); - swap_endian_data(c, data_len, data); + swap_endian_data(c, data_len, data, 1); } else bam_write(fp, &block_len, 4); bam_write(fp, x, BAM_CORE_SIZE); bam_write(fp, data, data_len); - if (bam_is_be) swap_endian_data(c, data_len, data); + if (bam_is_be) swap_endian_data(c, data_len, data, 0); return 4 + block_len; }