r762: cleanup for the new release; unfinished
It will take to make the documentation ready.
This commit is contained in:
Heng Li
parent
cfe6996173
commit
39a6cd5bb0
40
Makefile
40
Makefile
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@ -37,3 +37,43 @@ depend:
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( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
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# DO NOT DELETE THIS LINE -- make depend depends on it.
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QSufSort.o: QSufSort.h
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bamlite.o: bamlite.h malloc_wrap.h
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bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h
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bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kseq.h
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bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
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bwamem.o: ksort.h utils.h kbtree.h
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bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h
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bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
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bwamem_pair.o: utils.h ksw.h
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bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
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bwape.o: ksw.h khash.h
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bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
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bwase.o: bwa.h ksw.h
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bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
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bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
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bwt_gen.o: QSufSort.h malloc_wrap.h
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bwt_lite.o: bwt_lite.h malloc_wrap.h
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bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
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bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
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bwtindex.o: bntseq.h bwt.h utils.h malloc_wrap.h
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bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
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bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
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bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
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bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
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bwtsw2_core.o: khash.h ksort.h
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bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
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bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
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bwtsw2_pair.o: malloc_wrap.h ksw.h
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example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
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fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
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is.o: malloc_wrap.h
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kopen.o: malloc_wrap.h
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kstring.o: kstring.h malloc_wrap.h
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ksw.o: ksw.h malloc_wrap.h
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main.o: kstring.h malloc_wrap.h utils.h
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malloc_wrap.o: malloc_wrap.h
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pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
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test-extend.o: ksw.h
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utils.o: utils.h ksort.h malloc_wrap.h kseq.h
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49
NEWS
49
NEWS
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@ -1,3 +1,52 @@
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Release 0.7.9 (11 May, 2014)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This release brings several major changes to BWA-MEM. Notably, BWA-MEM
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now formally supports PacBio reads. It generally runs faster at a minor cost of
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accuracy. The speedup is more significant when GRCh38 is in use. More
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specifically:
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* Support PacBio subreads to reference alignment. Although older BWA-MEM works
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with PacBio data in principle, the resultant alignments are frequently
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fragmented. In this release, we fine tuned existing methods and introduced
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new heuristics to improve PacBio alignment. These changes are not used by
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default. Users need to add option "-x pacbio" to enable the feature.
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* Support PacBio subread-to-subread alignment. The feature is enabled with
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option "-x pbread". In this mode, the output only gives the overlapping
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region between a pair of reads without detailed alignment.
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* Output alternative hits in the XA tag if there are not so many such hits.
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This feature is originally implemented in BWA-backtrack.
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* EXPERIMENTAL feature to support mapping to ALT contigs in GRCh38. We prodive
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a script to postprocess hits in the XA tag to adjust the mapping quality and
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generate new primary alignments to all overlapping ALT contigs. We would NOT
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recommended this feature for production uses.
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* Improved alignments to many short reference sequences. Older BWA-MEM may
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generate an alignment bridging two or more adjacent reference sequences.
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Such alignments are split at a later step as postprocessing. This approach
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is complex and does not always work. This release forbids these alignments
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from the very beginning. BWA-MEM should not produce an alignment bridging
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two or more reference sequences any more.
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* Reduced the maximum seed occurrence from 10000 to 500. Reduced the maximum
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number of Smith-Waterman mate rescue from 100 to 50. Added a heuristic to
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lower the mapping quality if a read contains seeds with excessive
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occurrences. These changes make BWA-MEM XXX faster for mapping short reads
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to GRCh37 and XXX faster to GRCh38.
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* Added an option "-Y" to use soft clipping for supplementary alignments.
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* Bugfix: incomplete alignment extension in corner cases.
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* Bugfix: integer overflow when aligning low query sequences.
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(0.7.9: 11 May 2014, r777)
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Release 0.7.8 (31 March, 2014)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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36
README.md
36
README.md
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@ -14,7 +14,7 @@ BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
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sequence reads up to 100bp, while the rest two for longer sequences ranged from
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70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as the support of
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long reads and chimeric alignment, but BWA-MEM, which is the latest, is
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generally recommended for high-quality queries as it is faster and more
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generally recommended as it is faster and more
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accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp
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Illumina reads.
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@ -59,6 +59,38 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
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###Frequently asked questions (FAQs)
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####What types of data does BWA work with?
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BWA works with a variety types of DNA sequence data, though the optimal
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algorithm and setting may vary. The following list gives the recommended
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settings:
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* Illumina/454/IonTorrent single-end reads longer than ~70bp or assembly
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contigs up to a few megabases:
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bwa mem ref.fa reads.fq > aln.sam
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* Illumina/454/IonTorrent paired-end reads longer than ~70bp:
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bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
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* PacBio subreads to a reference genome:
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bwa mem -x pacbio ref.fa reads.fq > aln.sam
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* PacBio subreads to themselves (the output is not SAM):
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bwa mem -x pbread reads.fq reads.fq > overlap.pas
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* Illumina single-end reads no longer than ~70bp:
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bwa aln ref.fa reads.fq > reads.sai; bwa samse ref.fa reads.sai reads.fq > aln-se.sam
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* Illumina paired-end reads no longer than ~70bp:
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bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai
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bwa samse ref.fa reads.sai reads.fq > aln-pe.sam
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####How to map sequences to GRCh38 with ALT contigs?
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BWA-backtrack and BWA-MEM partially support mapping to a reference containing
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@ -91,6 +123,8 @@ highly repetitive regions as these hits will not be reported with option
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`-h50`. `bwa-helper.js` is a prototype implementation not recommended for
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production uses.
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[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
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[2]: https://github.com/lh3/bwa
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[3]: http://sourceforge.net/projects/bio-bwa/files/
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12
bwa.1
12
bwa.1
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@ -1,4 +1,4 @@
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.TH bwa 1 "31 March 2014" "bwa-0.7.8" "Bioinformatics tools"
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.TH bwa 1 "11 May 2014" "bwa-0.7.9" "Bioinformatics tools"
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.SH NAME
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.PP
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bwa - Burrows-Wheeler Alignment Tool
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@ -248,6 +248,11 @@ Don't output alignment with score lower than
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.IR INT .
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This option affects output and occasionally SAM flag 2. [30]
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.TP
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.BI -h \ INT
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If a query has not more than
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.I INT
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hits with score higher than 80% of the best hit, output them all in the XA tag [5]
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.TP
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.B -a
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Output all found alignments for single-end or unpaired paired-end reads. These
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alignments will be flagged as secondary alignments.
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@ -258,6 +263,11 @@ transfer read meta information (e.g. barcode) to the SAM output. Note that the
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FASTA/Q comment (the string after a space in the header line) must conform the SAM
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spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
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.TP
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.B -Y
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Use soft clipping CIGAR operation for supplementary alignments. By default, BWA-MEM
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uses soft clipping for the primary alignment and hard clipping for
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supplementary alignments.
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.TP
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.B -M
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Mark shorter split hits as secondary (for Picard compatibility).
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.TP
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1
bwamem.c
1
bwamem.c
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@ -64,6 +64,7 @@ mem_opt_t *mem_opt_init()
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o->max_ins = 10000;
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o->mask_level = 0.50;
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o->drop_ratio = 0.50;
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o->XA_drop_ratio = 0.80;
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o->split_factor = 1.5;
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o->chunk_size = 10000000;
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o->n_threads = 1;
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1
bwamem.h
1
bwamem.h
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@ -42,6 +42,7 @@ typedef struct {
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int chunk_size; // process chunk_size-bp sequences in a batch
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float mask_level; // regard a hit as redundant if the overlap with another better hit is over mask_level times the min length of the two hits
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float drop_ratio; // drop a chain if its seed coverage is below drop_ratio times the seed coverage of a better chain overlapping with the small chain
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float XA_drop_ratio; // when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
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float mask_level_redun;
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float mapQ_coef_len;
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int mapQ_coef_fac;
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@ -115,7 +115,7 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
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cnt = calloc(a->n, sizeof(int));
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for (i = 0, tot = 0; i < a->n; ++i) {
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int j = a->a[i].secondary;
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if (j >= 0 && a->a[i].score >= a->a[j].score * opt->drop_ratio)
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if (j >= 0 && a->a[i].score >= a->a[j].score * opt->XA_drop_ratio)
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++cnt[j], ++tot;
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}
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if (tot == 0) goto end_gen_alt;
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@ -123,7 +123,7 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
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for (i = 0; i < a->n; ++i) {
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mem_aln_t t;
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int j = a->a[i].secondary;
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if (j < 0 || a->a[i].score < a->a[j].score * opt->drop_ratio) continue; // we don't process the primary alignments as they will be converted to SAM later
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if (j < 0 || a->a[i].score < a->a[j].score * opt->XA_drop_ratio) continue; // we don't process the primary alignments as they will be converted to SAM later
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if (cnt[j] > opt->max_hits) continue;
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t = mem_reg2aln(opt, bns, pac, l_query, query, &a->a[i]);
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kputs(bns->anns[t.rid].name, &aln[j]);
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@ -159,6 +159,7 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, " -h INT if #hits < INT, output all in the XA tag [%d]\n", opt->max_hits);
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fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
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fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
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fprintf(stderr, " -Y use soft clipping for supplementary alignments\n");
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fprintf(stderr, " -M mark shorter split hits as secondary\n\n");
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fprintf(stderr, " -I FLOAT[,FLOAT[,INT[,INT]]]\n");
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fprintf(stderr, " specify the mean, standard deviation (10%% of the mean if absent), max\n");
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