Package: python-pysam
Version: 0.7.7-1
Tags: sid patch
Severity: important
Justification: FTBFS
User: [email protected]
Usertags: mips-patch
Control: block -1 by 753485
While trying to build python-pysam on mips/mipsel, build fails on testing.
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
The cause of test failures are issues in both 'samtools' and 'python-pysam'
packages.
For python-pysam to work samtools has to be fixed first since 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).
python-pysam has unaligned memory access and system endianness related issues
as well.
I have attached patches that fix this.
With samtools fixed (with solution proposed at
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753485), and attached patches
are applied to python-pysam, I have successfully built python-pysam on
mips and mipsel.
Could you consider including these patches?
Best regards,
Aleksandar Zlicic
Index: python-pysam-0.7.7/samtools/bam_import.c.pysam.c
===================================================================
--- python-pysam-0.7.7.orig/samtools/bam_import.c.pysam.c
+++ python-pysam-0.7.7/samtools/bam_import.c.pysam.c
@@ -367,6 +367,9 @@ 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];
+ uint8_t tmpData[8];
+ int j;
+
z += str->l + 1;
if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
parse_error(fp->n_lines, "missing colon in auxiliary data");
@@ -412,15 +415,35 @@ int sam_read1(tamFile fp, bam_header_t *
}
}
} else if (type == 'f') {
+#ifdef ALLOW_UAC
s = alloc_data(b, doff + 5) + doff;
*s++ = 'f';
*(float*)s = (float)atof(str->s + 5);
s += 4; doff += 5;
+#else
+ float *ptmpData = (float*)&tmpData;
+ s = alloc_data(b, doff + 5) + doff;
+ *s++ = 'f';
+ for(j=0;j<4;j++) tmpData[j]=s[j];
+ *ptmpData = (float)atof(str->s + 5);
+ for(j=0;j<4;j++) s[j] = tmpData[j];
+ s += 4; doff += 5;
+ #endif
} else if (type == 'd') {
+#ifdef ALLOW_UAC
s = alloc_data(b, doff + 9) + doff;
*s++ = 'd';
*(float*)s = (float)atof(str->s + 9);
s += 8; doff += 9;
+#else
+ float *ptmpData = (float*)&tmpData;
+ s = alloc_data(b, doff + 9) + doff;
+ *s++ = 'd';
+ for(j=0;j<8;j++) tmpData[j]=s[j];
+ *ptmpData = (float)atof(str->s + 9);
+ for(j=0;j<8;j++) s[j] = tmpData[j];
+ s += 8; doff += 9;
+#endif
} else if (type == 'Z' || type == 'H') {
int size = 1 + (str->l - 5) + 1;
if (type == 'H') { // check whether the hex string is valid
Index: python-pysam-0.7.7/samtools/bam.h
===================================================================
--- python-pysam-0.7.7.orig/samtools/bam.h
+++ python-pysam-0.7.7/samtools/bam.h
@@ -70,6 +70,12 @@ typedef gzFile bamFile;
/* no bam_write/bam_tell/bam_seek() here */
#endif
+#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
+# define ALLOW_UAC
+#else
+# undef ALLOW_UAC
+#endif
+
/*! @typedef
@abstract Structure for the alignment header.
@field n_targets number of reference sequences
Index: python-pysam-0.7.7/samtools/bam_aux.c.pysam.c
===================================================================
--- python-pysam-0.7.7.orig/samtools/bam_aux.c.pysam.c
+++ python-pysam-0.7.7/samtools/bam_aux.c.pysam.c
@@ -180,7 +180,18 @@ float bam_aux2f(const uint8_t *s)
int type;
type = *s++;
if (s == 0) return 0.0;
+#ifdef ALLOW_UAC
if (type == 'f') return *(float*)s;
+#else
+ if (type == 'f')
+ {
+ uint8_t tmpData[4];
+ int j;
+ float *ptmpData = (float*)&tmpData;
+ for(j=0;j<4;j++) tmpData[j]=s[j];
+ return *ptmpData;
+ }
+#endif
else return 0.0;
}
@@ -189,7 +200,19 @@ double bam_aux2d(const uint8_t *s)
int type;
type = *s++;
if (s == 0) return 0.0;
+#ifdef ALLOW_UAC
if (type == 'd') return *(double*)s;
+#else
+ if (type == 'd')
+ {
+ uint8_t tmpData[8];
+ int j;
+ double *ptmpData = (double*)&tmpData;
+ for(j=0;j<8;j++) tmpData[j]=s[j];
+ return *ptmpData;
+
+ }
+#endif
else return 0.0;
}
Index: python-pysam-0.7.7/pysam/csamtools.pyx
===================================================================
--- python-pysam-0.7.7.orig/pysam/csamtools.pyx
+++ python-pysam-0.7.7/pysam/csamtools.pyx
@@ -2763,7 +2763,7 @@ cdef class AlignedRead:
src = self._delegate
- fmts, args = ["<"], []
+ fmts, args = ["="], []
if tags != None:
Index: python-pysam-0.7.7/samtools/bam.c.pysam.c
===================================================================
--- python-pysam-0.7.7.orig/samtools/bam.c.pysam.c
+++ python-pysam-0.7.7/samtools/bam.c.pysam.c
@@ -159,7 +159,7 @@ 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);
@@ -176,17 +176,19 @@ 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;
+ }
}
}
@@ -219,7 +221,7 @@ 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;
}
@@ -242,11 +244,11 @@ 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;
}
