Package: samtools
Version: 0.1.19-1
Tags: sid patch
Severity: important
User: [email protected]
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;
}
