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commit 68cd7e53b4340f38e98b0621c9a3a37e253992e9 Author: Anders Kaplan <[email protected]> Date: Mon Jul 3 23:09:19 2017 +0200 Minor reformatting. --- cram/cram_codecs.c | 2 +- cram/cram_decode.c | 16 ++++++++-------- cram/cram_encode.c | 2 +- cram/cram_io.c | 2 +- realn.c | 2 +- sam.c | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-) diff --git a/cram/cram_codecs.c b/cram/cram_codecs.c index 4fe9574..758de44 100644 --- a/cram/cram_codecs.c +++ b/cram/cram_codecs.c @@ -239,7 +239,7 @@ static inline unsigned int get_bits_MSB(cram_block *block, int nbits) { * for it elsewhere.) */ static int store_bits_MSB(cram_block *block, unsigned int val, int nbits) { - /* fprintf(stderr, " store_bits: %02x %d\n", val, nbits); */ + //fprintf(stderr, " store_bits: %02x %d\n", val, nbits); /* * Use slow mode until we tweak the huffman generator to never generate diff --git a/cram/cram_decode.c b/cram/cram_decode.c index 513cb51..9571326 100644 --- a/cram/cram_decode.c +++ b/cram/cram_decode.c @@ -2741,11 +2741,11 @@ int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, // As we grow blocks we overallocate by up to 50%. So shrink // back to their final sizes here. // -// fprintf(stderr, "%d %d // %d %d // %d %d // %d %d\n", -// (int)s->seqs_blk->byte, (int)s->seqs_blk->alloc, -// (int)s->qual_blk->byte, (int)s->qual_blk->alloc, -// (int)s->name_blk->byte, (int)s->name_blk->alloc, -// (int)s->aux_blk->byte, (int)s->aux_blk->alloc); + //fprintf(stderr, "%d %d // %d %d // %d %d // %d %d\n", + // (int)s->seqs_blk->byte, (int)s->seqs_blk->alloc, + // (int)s->qual_blk->byte, (int)s->qual_blk->alloc, + // (int)s->name_blk->byte, (int)s->name_blk->alloc, + // (int)s->aux_blk->byte, (int)s->aux_blk->alloc); BLOCK_RESIZE_EXACT(s->seqs_blk, BLOCK_SIZE(s->seqs_blk)+1); BLOCK_RESIZE_EXACT(s->qual_blk, BLOCK_SIZE(s->qual_blk)+1); BLOCK_RESIZE_EXACT(s->name_blk, BLOCK_SIZE(s->name_blk)+1); @@ -3121,9 +3121,9 @@ static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) { hts_tpool_result *res; cram_decode_job *j; -// fprintf(stderr, "Thread pool len = %d, %d\n", -// hts_tpool_results_queue_len(fd->rqueue), -// hts_tpool_results_queue_sz(fd->rqueue)); + //fprintf(stderr, "Thread pool len = %d, %d\n", + // hts_tpool_results_queue_len(fd->rqueue), + // hts_tpool_results_queue_sz(fd->rqueue)); if (fd->ooc && hts_tpool_process_empty(fd->rqueue)) return NULL; diff --git a/cram/cram_encode.c b/cram/cram_encode.c index e667d21..2d78732 100644 --- a/cram/cram_encode.c +++ b/cram/cram_encode.c @@ -1446,7 +1446,7 @@ int cram_encode_container(cram_fd *fd, cram_container *c) { h->codecs[DS_CF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_CF]), c->stats[DS_CF], E_INT, NULL, fd->version); -// fprintf(stderr, "=== RN ===\n"); + //fprintf(stderr, "=== RN ===\n"); // h->codecs[DS_RN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RN]), // c->stats[DS_RN], E_BYTE_ARRAY, NULL, // fd->version); diff --git a/cram/cram_io.c b/cram/cram_io.c index d41e76c..bf50130 100644 --- a/cram/cram_io.c +++ b/cram/cram_io.c @@ -786,7 +786,7 @@ cram_block *cram_read_block(cram_fd *fd) { if (-1 == itf8_decode_crc(fd, &b->comp_size, &crc)) { free(b); return NULL; } if (-1 == itf8_decode_crc(fd, &b->uncomp_size, &crc)) { free(b); return NULL; } - // fprintf(stderr, " method %d, ctype %d, cid %d, csize %d, ucsize %d\n", + //fprintf(stderr, " method %d, ctype %d, cid %d, csize %d, ucsize %d\n", // b->method, b->content_type, b->content_id, b->comp_size, b->uncomp_size); if (b->method == RAW) { diff --git a/realn.c b/realn.c index d856f3c..a33acde 100644 --- a/realn.c +++ b/realn.c @@ -78,7 +78,7 @@ int sam_cap_mapq(bam1_t *b, const char *ref, int ref_len, int thres) if (t > thres) return -1; if (t < 0) t = 0; t = sqrt((thres - t) / thres) * thres; -// fprintf(stderr, "%s %lf %d\n", bam_get_qname(b), t, q); + //fprintf(stderr, "%s %lf %d\n", bam_get_qname(b), t, q); return (int)(t + .499); } diff --git a/sam.c b/sam.c index 5e9c20d..7028b92 100644 --- a/sam.c +++ b/sam.c @@ -1852,7 +1852,7 @@ static inline int resolve_cigar2(bam_pileup1_t *p, int32_t pos, cstate_t *s) uint32_t *cigar = bam_get_cigar(b); int k; // determine the current CIGAR operation -// fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam_get_qname(b), pos, s->end, s->k, s->x, s->y); + //fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam_get_qname(b), pos, s->end, s->k, s->x, s->y); if (s->k == -1) { // never processed if (c->n_cigar == 1) { // just one operation, save a loop if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
