This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libssw.
commit 0f3f755ac31a8fd1d3bc67f1f6bb065a7423ffa0 Author: Sascha Steinbiss <[email protected]> Date: Fri Jun 24 14:59:47 2016 +0000 Imported Upstream version 1.0 --- src/main.c | 4 ++-- src/ssw.c | 17 ----------------- 2 files changed, 2 insertions(+), 19 deletions(-) diff --git a/src/main.c b/src/main.c index a394be4..2ed7cc1 100644 --- a/src/main.c +++ b/src/main.c @@ -1,7 +1,7 @@ /* main.c * Created by Mengyao Zhao on 06/23/11. * Version 0.1.5 - * Last revision by Mengyao Zhao on 02/23/16. + * Last revision by Mengyao Zhao on 06/24/16. */ #include <stdlib.h> @@ -364,7 +364,7 @@ int main (int argc, char * const argv[]) { mat = mata; } - fprintf(stderr, "query: %s\n", argv[optind + 1]); + //fprintf(stderr, "query: %s\n", argv[optind + 1]); read_fp = gzopen(argv[optind + 1], "r"); if (! read_fp) { diff --git a/src/ssw.c b/src/ssw.c index bf31ba5..825c39b 100644 --- a/src/ssw.c +++ b/src/ssw.c @@ -181,13 +181,10 @@ static alignment_end* sw_sse2_byte (const int8_t* ref, step = -1; } for (i = begin; LIKELY(i != end); i += step) { -//fprintf(stderr, "%d", ref[i]); int32_t cmp; __m128i e, vF = vZero, vMaxColumn = vZero; /* Initialize F value to 0. Any errors to vH values will be corrected in the Lazy_F loop. */ -// max16(maxColumn[i], vMaxColumn); -// fprintf(stderr, "middle[%d]: %d\n", i, maxColumn[i]); __m128i vH = pvHStore[segLen - 1]; vH = _mm_slli_si128 (vH, 1); /* Shift the 128-bit value in vH left by 1 byte. */ @@ -202,11 +199,6 @@ static alignment_end* sw_sse2_byte (const int8_t* ref, for (j = 0; LIKELY(j < segLen); ++j) { vH = _mm_adds_epu8(vH, _mm_load_si128(vP + j)); vH = _mm_subs_epu8(vH, vBias); /* vH will be always > 0 */ - // max16(maxColumn[i], vH); - // fprintf(stderr, "H[%d]: %d\n", i, maxColumn[i]); -// int8_t* t; -// int32_t ti; -//for (t = (int8_t*)&vH, ti = 0; ti < 16; ++ti) fprintf(stderr, "%d\t", *t++); /* Get max from vH, vE and vF. */ e = _mm_load_si128(pvE + j); @@ -214,10 +206,6 @@ static alignment_end* sw_sse2_byte (const int8_t* ref, vH = _mm_max_epu8(vH, vF); vMaxColumn = _mm_max_epu8(vMaxColumn, vH); - // max16(maxColumn[i], vMaxColumn); - // fprintf(stderr, "middle[%d]: %d\n", i, maxColumn[i]); -// for (t = (int8_t*)&vMaxColumn, ti = 0; ti < 16; ++ti) fprintf(stderr, "%d\t", *t++); - /* Save vH values. */ _mm_store_si128(pvHStore + j, vH); @@ -290,7 +278,6 @@ static alignment_end* sw_sse2_byte (const int8_t* ref, /* Record the max score of current column. */ max16(maxColumn[i], vMaxColumn); - // fprintf(stderr, "maxColumn[%d]: %d\n", i, maxColumn[i]); if (maxColumn[i] == terminate) break; } @@ -322,7 +309,6 @@ static alignment_end* sw_sse2_byte (const int8_t* ref, edge = (end_ref - maskLen) > 0 ? (end_ref - maskLen) : 0; for (i = 0; i < edge; i ++) { -// fprintf (stderr, "maxColumn[%d]: %d\n", i, maxColumn[i]); if (maxColumn[i] > bests[1].score) { bests[1].score = maxColumn[i]; bests[1].ref = i; @@ -330,7 +316,6 @@ static alignment_end* sw_sse2_byte (const int8_t* ref, } edge = (end_ref + maskLen) > refLen ? refLen : (end_ref + maskLen); for (i = edge + 1; i < refLen; i ++) { -// fprintf (stderr, "refLen: %d\tmaxColumn[%d]: %d\n", refLen, i, maxColumn[i]); if (maxColumn[i] > bests[1].score) { bests[1].score = maxColumn[i]; bests[1].ref = i; @@ -606,7 +591,6 @@ static cigar* banded_sw (const int8_t* ref, temp1 = i == 0 ? -weight_gapO : h_b[e] - weight_gapO; temp2 = i == 0 ? -weight_gapE : e_b[e] - weight_gapE; e_b[u] = temp1 > temp2 ? temp1 : temp2; - //fprintf(stderr, "de: %d\twidth_d: %d\treadLen: %d\ts2:%lu\n", de, width_d, readLen, s2); direction_line[de] = temp1 > temp2 ? 3 : 2; temp1 = h_c[b] - weight_gapO; @@ -821,7 +805,6 @@ s_align* ssw_align (const s_profile* prof, } r->score1 = bests[0].score; r->ref_end1 = bests[0].ref; -//fprintf(stderr, "0based ref_end: %d\n", r->ref_end1); r->read_end1 = bests[0].read; if (maskLen >= 15) { r->score2 = bests[1].score; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libssw.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
