// Function to compare reads and determine which one is < the other
static inline int bam1_lt(const bam1_p a, const bam1_p b)
{
if (g_is_by_qname) {
int t = strnum_cmp(bam_get_qname(a), bam_get_qname(b));
return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0)));
} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam_is_rev(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam_is_rev(b)));
}
static inline int bam1_lt(const bam1_p a, const bam1_p b)
{
if (g_is_by_qname) {
int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos))));
} else return (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos));
}
// Function to compare reads in the heap and determine which one is < the other
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
int t;
if (a.b == NULL || b.b == NULL) return a.b == NULL? 1 : 0;
t = strnum_cmp(bam_get_qname(a.b), bam_get_qname(b.b));
return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0)));
} else return __pos_cmp(a, b);
}
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
int t;
if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
return (t > 0 || (t == 0 && __pos_cmp(a, b)));
} else return __pos_cmp(a, b);
}
static inline int bam1_lt(const bam1_p a, const bam1_p b)
{
if (g_is_by_qname) {
int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
if (t != 0) return (t < 0);
if(1 == (a->core.flag&BAM_FPAIRED) && 1 == (b->core.flag&BAM_FPAIRED)) {
if(a->core.flag&BAM_FREAD1) return (0 < 1);
else return (1 < 0);
}
else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
}
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
int t;
if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
if (t != 0) return (0 > t);
if(1 == (a.b->core.flag&BAM_FPAIRED) && 1 == (b.b->core.flag&BAM_FPAIRED)) {
if(a.b->core.flag&BAM_FREAD1) return (0 < 1);
else return (1 < 0);
}
else return __pos_cmp(a, b);
} else return __pos_cmp(a, b);
}
int b2g_bam_qname_cmp(void* a, void* b) {
return strnum_cmp(bam1_qname((bam1_t*)a), bam1_qname((bam1_t*)b));
}
