DELTA 397850 0 463 SVN9K  _iPbwaENDREP DELTA SVN 2 x^P]o0}% 3iR'/7E9`O}sFNT|m4\}oU-Ң#Fw3Z~=<d|B_WQF fF6ټgKF!‰V`,D_kdIs1͡?nPV{Wr%7Zbٱ<~ :9;a lzϰf^ x2$PZzv >YݫNZPZ7czm/VY+!qk'֦C5+wY(5u-ugF[3VmǕ=~/sEON=>ҟܣ#|O=d~F}5kfz^$Je[]c:TʴENDREP DELTA SVNSHA256 (bwa-0.7.9a.tar.bz2) = f5ad30e4e5ea86a8dcd6febcb6f620a75c82b03024f64a572017c295a962eadc SIZE (bwa-0.7.9a.tar.bz2) = 166193 ENDREP DELTA SVN$&$$--- Makefile.orig 2014-05-19 13:11:41 UTC +++ Makefile @@ -1,6 +1,6 @@ -CC= gcc +CC?= gcc #CC= clang --analyze -CFLAGS= -g -Wall -Wno-unused-function -O2 +CFLAGS?= -g -Wall -Wno-unused-function -O2 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS AR= ar DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) ENDREP DELTA SVNoqoo--- bwt_lite.c.orig 2014-05-19 13:11:41 UTC +++ bwt_lite.c @@ -48,7 +48,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uin } { // generate cnt_table for (i = 0; i != 256; ++i) { - u_int32_t j, x = 0; + uint32_t j, x = 0; for (j = 0; j != 4; ++j) x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3); b->cnt_table[i] = x; ENDREP DELTA SVNPRPP--- bwtgap.c.orig 2014-02-25 21:20:01 UTC +++ bwtgap.c @@ -58,7 +58,7 @@ static inline void gap_push(gap_stack_t q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries); } p = q->stack + q->n_entries; - p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l; + p->info = (uint32_t)score<<21 | i; p->k = k; p->l = l; p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape; p->n_ins = n_ins; p->n_del = n_del; p->state = state; ENDREP DELTA SVN]_]]--- bwtgap.h.orig 2014-02-25 21:20:01 UTC +++ bwtgap.h @@ -5,9 +5,9 @@ #include "bwtaln.h" typedef struct { // recursion stack - u_int32_t info; // score<<21 | i - u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6; - u_int32_t n_ins:16, n_del:16; + uint32_t info; // score<<21 | i + uint32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6; + uint32_t n_ins:16, n_del:16; int last_diff_pos; bwtint_t k, l; // (k,l) is the SA region of [i,n-1] } gap_entry_t; ENDREP DELTA SVNqsqqBWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). 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