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This commit is contained in:
Heng Li 2013-02-28 00:58:24 -05:00
parent f3cff1c609
commit 39fcde9c19
2 changed files with 20 additions and 10 deletions
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25
NEWS
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@ -13,23 +13,32 @@ task given longer reads, either, and the edit-distance criterion is arguably
not as important in long-read alignment. not as important in long-read alignment.
In addition to the algorithmic improvements, BWA-SW also implements a few In addition to the algorithmic improvements, BWA-SW also implements a few
handy features, some of which are experimental: handy features in practical aspects:
1. BWA-MEM automatically infers pair orientation from a batch of single-end 1. BWA-MEM automatically switches between local and glocal (global wrt reads;
local wrt reference) alignment. It reports the end-to-end glocal alignment
if the glocal alignment is not much worse than the optimal local alignment.
Glocal alignment reduces reference bias.
2. BWA-MEM automatically infers pair orientation from a batch of single-end
alignments. It allows more than one orientations if there are sufficient alignments. It allows more than one orientations if there are sufficient
reads supporting them. This feature has not been tested on reads from supporting reads. This feature has not been tested on reads from Illumina
Illumina jumping library yet. jumping library yet. (EXPERIMENTAL)
2. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It 3. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It
is possible to convert a name-sorted BAM to an interleaved fastq on the fly is possible to convert a name-sorted BAM to an interleaved fastq on the fly
and feed the data stream to BWA-MEM for mapping. and feed the data stream to BWA-MEM for mapping.
3. BWA-MEM optionally copies FASTA/Q comments to the final SAM output. This 4. BWA-MEM optionally copies FASTA/Q comments to the final SAM output, which
helps to transfer individual read annotations to the output. helps to transfer individual read annotations to the output.
4. BWA-MEM supports more advanced piping. Users can now run: 5. BWA-MEM supports more advanced piping. Users can now run:
(bwa mem ref.fa '<bzcat r1.fq.bz2' '<bzcat r2.fq.bz2') to map bzip'd read (bwa mem ref.fa '<bzcat r1.fq.bz2' '<bzcat r2.fq.bz2') to map bzip'd read
files without replying on the bash feature. files without replying on bash features.
6. BWA-MEM provides a few basic APIs for single-end mapping. The `example.c'
program in the source code directory implements a full single-end mapper in
50 lines of code.
The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM
for production use yet. However, when the implementation becomes stable after a for production use yet. However, when the implementation becomes stable after a

5
example.c
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@ -33,10 +33,11 @@ int main(int argc, char *argv[])
mem_aln_t a; mem_aln_t a;
if (ar.a[i].secondary >= 0) continue; // skip secondary alignments if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, (uint8_t*)ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, (uint8_t*)ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
// print alignment
printf("%s\t%c\t%s\t%d\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, a.pos, a.mapq); printf("%s\t%c\t%s\t%d\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, a.pos, a.mapq);
for (k = 0; k < a.n_cigar; ++k) for (k = 0; k < a.n_cigar; ++k) // print CIGAR
printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]); printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
printf("\t%d\n", a.NM); printf("\t%d\n", a.NM); // print edit distance
free(a.cigar); // don't forget to deallocate CIGAR free(a.cigar); // don't forget to deallocate CIGAR
} }
free(ar.a); // and deallocate the hit list free(ar.a); // and deallocate the hit list