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sam_format1 : replace if/then with switch/case #704

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sam_format1 : replace if/then with switch/case #704

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189 changes: 108 additions & 81 deletions sam.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1517,92 +1517,119 @@ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
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;
} else if (type == 'S') {
if (end - s >= 2) {
kputsn("i:", 2, str);
kputuw(le_to_u16(s), str);
s += 2;
} else goto bad_aux;
} else if (type == 's') {
if (end - s >= 2) {
kputsn("i:", 2, str);
kputw(le_to_i16(s), str);
s += 2;
} else goto bad_aux;
} else if (type == 'I') {
if (end - s >= 4) {
kputsn("i:", 2, str);
kputuw(le_to_u32(s), str);
s += 4;
} else goto bad_aux;
} else if (type == 'i') {
if (end - s >= 4) {
kputsn("i:", 2, str);
kputw(le_to_i32(s), str);
s += 4;
} else goto bad_aux;
} else if (type == 'f') {
if (end - s >= 4) {
ksprintf(str, "f:%g", le_to_float(s));
s += 4;
} else goto bad_aux;

} else if (type == 'd') {
if (end - s >= 8) {
ksprintf(str, "d:%g", le_to_double(s));
s += 8;
} else goto bad_aux;
} else if (type == 'Z' || type == 'H') {
kputc(type, str); kputc(':', str);
while (s < end && *s) kputc(*s++, str);
if (s >= end)
goto bad_aux;
++s;
} else if (type == 'B') {
uint8_t sub_type = *(s++);
int sub_type_size = aux_type2size(sub_type);
uint32_t n;
if (sub_type_size == 0 || end - s < 4)
goto bad_aux;
n = le_to_u32(s);
s += 4; // now points to the start of the array
if ((end - s) / sub_type_size < n)
goto bad_aux;
kputsn("B:", 2, str); kputc(sub_type, str); // write the typing
for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if"
kputc(',', str);
if ('c' == sub_type) { kputw(*(int8_t*)s, str); ++s; }
else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; }
else if ('s' == sub_type) { kputw(le_to_i16(s), str); s += 2; }
else if ('S' == sub_type) { kputw(le_to_u16(s), str); s += 2; }
else if ('i' == sub_type) { kputw(le_to_i32(s), str); s += 4; }
else if ('I' == sub_type) { kputuw(le_to_u32(s), str); s += 4; }
else if ('f' == sub_type) { kputd(le_to_float(s), str); s += 4; }
else goto bad_aux; // Unknown sub-type
#define LOG_ERROR_AUX do {\
hts_log_error("Corrupted aux data \"%c%c\" for read %.*s",\
key[0],key[1],\
b->core.l_qname, bam_get_qname(b));\
errno = EINVAL;\
return -1;\
} while(0)

switch(type) {
case 'A': {
kputsn("A:", 2, str);
kputc(*s, str);
++s;
break;
}
} else { // Unknown type
goto bad_aux;
}
case 'C': {
kputsn("i:", 2, str);
kputw(*s, str);
++s;
break;
}
case 'c': {
kputsn("i:", 2, str);
kputw(*(int8_t*)s, str);
++s;
break;
}
case 'S': {
if (end - s >= 2) {
kputsn("i:", 2, str);
kputuw(le_to_u16(s), str);
s += 2;
} else LOG_ERROR_AUX;
break;
}
case 's': {
if (end - s >= 2) {
kputsn("i:", 2, str);
kputw(le_to_i16(s), str);
s += 2;
} else LOG_ERROR_AUX;
break;
}
case 'I': {
if (end - s >= 4) {
kputsn("i:", 2, str);
kputuw(le_to_u32(s), str);
s += 4;
} else LOG_ERROR_AUX;
break;
}
case 'i': {
if (end - s >= 4) {
kputsn("i:", 2, str);
kputw(le_to_i32(s), str);
s += 4;
} else LOG_ERROR_AUX;
break;
}
case 'f': {
if (end - s >= 4) {
ksprintf(str, "f:%g", le_to_float(s));
s += 4;
} else LOG_ERROR_AUX;
break;
}
case 'd': {
if (end - s >= 8) {
ksprintf(str, "d:%g", le_to_double(s));
s += 8;
} else LOG_ERROR_AUX;
break;
}
case 'Z': case 'H': {
kputc(type, str); kputc(':', str);
while (s < end && *s) kputc(*s++, str);
if (s >= end)
LOG_ERROR_AUX;
++s;
break;
}
case 'B': {
uint8_t sub_type = *(s++);
int sub_type_size = aux_type2size(sub_type);
uint32_t n;
if (sub_type_size == 0 || end - s < 4)
LOG_ERROR_AUX;
n = le_to_u32(s);
s += 4; // now points to the start of the array
if ((end - s) / sub_type_size < n)
LOG_ERROR_AUX;
kputsn("B:", 2, str); kputc(sub_type, str); // write the typing

switch(sub_type) {
case 'c' : for (i = 0; i < n; ++i) {kputc(',', str); kputw(*(int8_t*)s, str); ++s; } break;
case 'C' : for (i = 0; i < n; ++i) {kputc(',', str); kputw(*(uint8_t*)s, str); ++s; } break;
case 's' : for (i = 0; i < n; ++i) {kputc(',', str); kputw(le_to_i16(s), str); s += 2; } break;
case 'S' : for (i = 0; i < n; ++i) {kputc(',', str); kputw(le_to_u16(s), str); s += 2; } break;
case 'i' : for (i = 0; i < n; ++i) {kputc(',', str); kputw(le_to_i32(s), str); s += 4; } break;
case 'I' : for (i = 0; i < n; ++i) {kputc(',', str); kputuw(le_to_u32(s), str); s += 4; } break;
case 'f' : for (i = 0; i < n; ++i) {kputc(',', str); kputd(le_to_float(s), str); s += 4; } break;
default: LOG_ERROR_AUX; break; // Unknown sub-type
}

break;
}
default: LOG_ERROR_AUX;break;
}
}
return str->l;

bad_aux:
hts_log_error("Corrupted aux data for read %.*s",
b->core.l_qname, bam_get_qname(b));
errno = EINVAL;
return -1;
#undef LOG_ERROR_AUX
}

int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b)
Expand Down