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fixed a long-existing bug in trimming

This commit is contained in:
Heng Li 2011-11-23 23:11:50 -05:00
parent 84aa3fa696
commit dec584d50b
4 changed files with 9 additions and 10 deletions
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6
bwa.1
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@ -46,7 +46,7 @@ command. It works for single-end reads only.
.SH COMMANDS AND OPTIONS
.TP
.B index
bwa index [-p prefix] [-a algoType] [-c] <in.db.fasta>
bwa index [-p prefix] [-a algoType] <in.db.fasta>
Index database sequences in the FASTA format.
@ -54,7 +54,7 @@ Index database sequences in the FASTA format.
.RS
.TP 10
.B -c
Build color-space index. The input fast should be in nucleotide space.
Build color-space index. The input fast should be in nucleotide space. (Disabled since 0.6.x)
.TP
.BI -p \ STR
Prefix of the output database [same as db filename]
@ -142,7 +142,7 @@ especially for short reads (~32bp).
.TP
.B -c
Reverse query but not complement it, which is required for alignment in
the color space.
the color space. (Disabled since 0.6.x)
.TP
.B -N
Disable iterative search. All hits with no more than

8
bwaseqio.c
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@ -73,16 +73,14 @@ void seq_reverse(int len, ubyte_t *seq, int is_comp)
int bwa_trim_read(int trim_qual, bwa_seq_t *p)
{
int s = 0, l, max = 0, max_l = p->len - 1;
int s = 0, l, max = 0, max_l = p->len;
if (trim_qual < 1 || p->qual == 0) return 0;
for (l = p->len - 1; l >= BWA_MIN_RDLEN - 1; --l) {
s += trim_qual - (p->qual[l] - 33);
if (s < 0) break;
if (s > max) {
max = s; max_l = l;
}
if (s > max) max = s, max_l = l;
}
p->clip_len = p->len = max_l + 1;
p->clip_len = p->len = max_l;
return p->full_len - p->len;
}

2
bwtaln.c
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@ -283,7 +283,7 @@ int bwa_aln(int argc, char *argv[])
fprintf(stderr, " -q INT quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
fprintf(stderr, " -f FILE file to write output to instead of stdout\n");
fprintf(stderr, " -B INT length of barcode\n");
fprintf(stderr, " -c input sequences are in the color space\n");
// fprintf(stderr, " -c input sequences are in the color space\n");
fprintf(stderr, " -L log-scaled gap penalty for long deletions\n");
fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n");
fprintf(stderr, " -I the input is in the Illumina 1.3+ FASTQ-like format\n");

3
bwtindex.c
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@ -65,7 +65,8 @@ int bwa_index(int argc, char *argv[])
fprintf(stderr, "Usage: bwa index [-a bwtsw|div|is] [-c] <in.fasta>\n\n");
fprintf(stderr, "Options: -a STR BWT construction algorithm: bwtsw or is [is]\n");
fprintf(stderr, " -p STR prefix of the index [same as fasta name]\n");
fprintf(stderr, " -c build color-space index\n\n");
// fprintf(stderr, " -c build color-space index\n");
fprintf(stderr, "\n");
fprintf(stderr, "Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
fprintf(stderr, " `-a div' do not work not for long genomes. Please choose `-a'\n");
fprintf(stderr, " according to the length of the genome.\n\n");