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bwa mem: read chunk size overflows for -t > 214 #155

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bwa mem: read chunk size overflows for -t > 214 #155

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deaea0e
promote chunk_size to int64_t to avoid int overflow at >214 threads
BenLangmead Oct 16, 2017
db35d8c
allow # bases read by bseq_read to exceed 2^31
BenLangmead Oct 16, 2017
2e3a068
promote actual_chunk_size to int64_t
BenLangmead Oct 16, 2017
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promote chunk_size to int64_t to avoid int overflow at >214 threads
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@BenLangmead
BenLangmead committed Oct 17, 2017
commit deaea0e595a6717525f1fad4cf3f47a8ffd07f29
2 changes: 1 addition & 1 deletion bwamem.h
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Expand Up @@ -43,7 +43,7 @@ typedef struct {
int max_occ; // skip a seed if its occurence is larger than this value
int max_chain_gap; // do not chain seed if it is max_chain_gap-bp away from the closest seed
int n_threads; // number of threads
int chunk_size; // process chunk_size-bp sequences in a batch
int64_t chunk_size; // process chunk_size-bp sequences in a batch
float mask_level; // regard a hit as redundant if the overlap with another better hit is over mask_level times the min length of the two hits
float drop_ratio; // drop a chain if its seed coverage is below drop_ratio times the seed coverage of a better chain overlapping with the small chain
float XA_drop_ratio; // when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
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