加入了获取reads和extension数据的代码
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parent
1e3965cb7d
commit
dd03596997
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@ -2,6 +2,8 @@
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*.txt
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*.sam
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*.log
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*.fa
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dataset/
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bwa
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test
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test64
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18
bwamem.c
18
bwamem.c
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@ -1482,7 +1482,23 @@ static void mem_collect_intv_batch(const mem_opt_t *opt, const FMTIndex *fmt, in
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#endif
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#ifdef FILTER_FULL_MATCH
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if (max_seed_len == len - start_N_num) goto collect_intv_end;
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if (max_seed_len == len - start_N_num) {
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#ifdef DEBUG_OUTPUT
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if (start_N_num == 0) {
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for (i = 0; i < len; ++i)
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fprintf(gfp1, "%c", "ACGT"[seq[i]]);
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fprintf(gfp1, "\n");
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#ifdef SHOW_DATA_PERF
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gdat[2]++;
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if (gdat[2] % 100 == 0) {
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fprintf(stderr, "reads num: %ld\n", gdat[2]);
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}
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#endif
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}
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#endif
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goto collect_intv_end;
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}
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#endif
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// 2. second pass: find MEMs inside a long SMEM
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30
fastmap.c
30
fastmap.c
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@ -92,7 +92,8 @@ int64_t gdat[100];
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#endif
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#ifdef DEBUG_OUTPUT
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FILE * gfp1, *gfp2, *gfp3;
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FILE * gfp1, *gfp2, *gfp3, *gfp4;
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FILE *gfq[4], *gft[4], *gfi[4];
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#endif
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extern unsigned char nst_nt4_table[256];
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@ -414,6 +415,18 @@ int main_mem(int argc, char *argv[])
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gfp1 = fopen("./fp1.txt", "w");
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gfp2 = fopen("./fp2.txt", "w");
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gfp3 = fopen("./fp3.txt", "w");
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gfp4 = fopen("./fp4.txt", "w");
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char fnbuf[1024];
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int ii;
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for (ii = 0; ii < 4; ++ii)
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{
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sprintf(fnbuf, "./ext_out/q_%d.fa", ii);
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gfq[ii] = fopen(fnbuf, "w");
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sprintf(fnbuf, "./ext_out/t_%d.fa", ii);
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gft[ii] = fopen(fnbuf, "w");
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sprintf(fnbuf, "./ext_out/i_%d.txt", ii);
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gfi[ii] = fopen(fnbuf, "w");
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}
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#endif
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#ifdef SHOW_PERF
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@ -776,13 +789,15 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, "time_process_seq: %0.2lf s\n", (time_work_kernel + time_work_sam) * 1.0 / proc_freq);
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fprintf(stderr, "time_seed_all: %0.2lf (%0.2lf, %0.2lf) s\n", avg_seed_all * 1.0 / proc_freq / opt->n_threads, min_seed_all * 1.0 / proc_freq, max_seed_all * 1.0 / proc_freq);
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fprintf(stderr, "time_seed_1: %0.2lf s\n", avg_seed_1 * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_seed_2: %0.2lf s\n", avg_seed_2 * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_seed_3: %0.2lf s\n", avg_seed_3 * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_sa: %0.2lf s\n", avg_sa * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_chain: %0.2lf s\n", avg_chain * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_bsw_all: %0.2lf (%0.2lf, %0.2lf) s\n", avg_bsw_all * 1.0 / proc_freq / opt->n_threads, min_bsw_all * 1.0 / proc_freq, max_bsw_all * 1.0 / proc_freq);
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fprintf(stderr, "\n");
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fprintf(stderr, "time_seed_1: %0.2lf s\n", avg_seed_1 * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_seed_2: %0.2lf s\n", avg_seed_2 * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_seed_3: %0.2lf s\n", avg_seed_3 * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_seed_chain: %0.2lf s\n", (avg_seed_all + avg_chain) * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "time_bsw: %0.2lf s\n", avg_bsw * 1.0 / proc_freq / opt->n_threads);
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fprintf(stderr, "\n");
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@ -798,6 +813,13 @@ int main_mem(int argc, char *argv[])
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fclose(gfp1);
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fclose(gfp2);
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fclose(gfp3);
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fclose(gfp4);
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for (ii = 0; ii < 4; ++ii)
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{
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fclose(gfq[ii]);
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fclose(gft[ii]);
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fclose(gfi[ii]);
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}
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#endif
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return 0;
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@ -6,8 +6,9 @@
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#include <immintrin.h>
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#include <emmintrin.h>
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#ifdef SHOW_PERF
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#ifdef DEBUG_OUTPUT
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extern FILE *gfp1, *gfp2, *gfp3;
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extern FILE *gfq[4], *gft[4], *gfi[4];
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#endif
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#define NO_VAL -1
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@ -172,6 +173,25 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
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tmp = fA1; fA1 = fA2; fA2 = tmp; \
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tmp = mA1; mA1 = mA2; mA2 = tmp;
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void write_query_target_sequence(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int h0, int fnum)
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{
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// 写到三个文件里，query.fa，target.fa，每行一个序列，info.txt，包含前缀得分h0，和长度信息qlen，tlen
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FILE *query_f = gfq[fnum],
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*target_f = gft[fnum],
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*info_f = gfi[fnum];
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const char seq_map[5] = {'A', 'C', 'G', 'T', 'N'};
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int i;
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// 处理query
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for (i = 0; i < qlen; ++i)
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fprintf(query_f, "%c", seq_map[query[i]]);
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fprintf(query_f, "\n");
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// 处理target
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for (i = 0; i < tlen; ++i)
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fprintf(target_f, "%c", seq_map[target[i]]);
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fprintf(target_f, "\n");
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// 处理其他信息
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fprintf(info_f, "%-8d%-8d%-8d\n", qlen, tlen, h0);
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}
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int ksw_extend2_avx2(int qlen, // query length 待匹配段碱基的query长度
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const uint8_t *query, // read碱基序列
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@ -201,6 +221,15 @@ int ksw_extend2_avx2(int qlen, // query length 待匹配段碱基的query长度
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#ifdef DEBUG_OUTPUT
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//fprintf(gfp1, "%d\n", qlen);
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if (qlen <= 30) {
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write_query_target_sequence(qlen, query, tlen, target, h0, 0);
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} else if (qlen < 60) {
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write_query_target_sequence(qlen, query, tlen, target, h0, 1);
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} else if (qlen < 90) {
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write_query_target_sequence(qlen, query, tlen, target, h0, 2);
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} else {
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write_query_target_sequence(qlen, query, tlen, target, h0, 3);
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}
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#endif
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if (qlen * a + h0 < 255) return ksw_extend2_avx2_u8(qlen, query, tlen, target, is_left, m, mat, o_del, e_del, o_ins, e_ins, a, b, w, end_bonus, zdrop, h0, _qle, _tle, _gtle, _gscore, _max_off, buf);
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17
run.sh
17
run.sh
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@ -3,12 +3,14 @@ thread=1
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#n_r2=~/data/fastq/dataset/na12878_wgs_150/bn2.fq
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#n_r1=~/data/fastq/dataset/na12878_wes_144/SRR25735653_1.fastq
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#n_r2=~/data/fastq/dataset/na12878_wes_144/SRR25735653_2.fastq
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#n_r1=~/data/fastq/dataset/na12878_wgs_150/n1.fq
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#n_r2=~/data/fastq/dataset/na12878_wgs_150/n2.fq
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#n_r1=~/data/fastq/dataset/na12878_wgs_150/s_1.fq
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#n_r2=~/data/fastq/dataset/na12878_wgs_150/s_2.fq
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#n_r1=~/data/fastq/dataset/na12878_wgs_101/na_1.fq
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#n_r2=~/data/fastq/dataset/na12878_wgs_101/na_2.fq
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n_r1=~/data/fastq/dataset/zy_wes/sn1.fq
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n_r2=~/data/fastq/dataset/zy_wes/sn2.fq
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n_r1=~/data/fastq/dataset/zy_wes/s_1.fq
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n_r2=~/data/fastq/dataset/zy_wes/s_2.fq
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#n_r1=~/data/fastq/dataset/zy_wes/bloodgDNA_r1.fastq
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#n_r2=~/data/fastq/dataset/zy_wes/bloodgDNA_r2.fastq
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#n_r1=~/data/fastq/zy/wgs/n1.fq
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@ -54,12 +56,13 @@ n_r2=~/data/fastq/dataset/zy_wes/sn2.fq
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#n_r2=~/fastq/diff_r2.fq
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#n_r1=~/fastq/d_r1.fq
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#n_r2=~/fastq/d_r2.fq
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reference=~/data/reference/human_g1k_v37_decoy.fasta
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reference=~/reference/human_g1k_v37_decoy.fasta
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#reference=~/data/reference/human_g1k_v37_decoy.fasta
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#out=./all.sam
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#out=./sn.sam
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#out=./ssn-x1.sam
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out=./out.sam
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#out=/dev/null
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#out=./out.sam
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out=/dev/null
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#out=./na12878.sam
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#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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# /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
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5
utils.h
5
utils.h
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@ -31,7 +31,7 @@
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#include <stdio.h>
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#include <zlib.h>
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#define USE_RDTSC 0
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#define USE_RDTSC 1
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#ifdef SHOW_PERF
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extern uint64_t time_process_data, time_read, time_write, time_compute,
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@ -48,7 +48,8 @@ extern int64_t gdat[100];
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#endif
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#ifdef DEBUG_OUTPUT
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extern FILE *gfp1, *gfp2, *gfp3;
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extern FILE *gfp1, *gfp2, *gfp3, *gfp4;
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extern FILE *gfq[4], *gft[4], *gfi[4];
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#endif
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#undef MAX
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