updated documentations

(prepare for release)

NEWS.md

@@ -11,25 +11,27 @@ For general uses, the single BWA binary still works like the old way.
 
 Another major addition to BWA-MEM is HLA typing, which made possible with the
 new ALT mapping strategy. Necessary data and programs are included in the
-binary release. The wrapper script also performs HLA typing when HLA genes are
-included in the reference genome as additional ALT contigs.
+binary release. The wrapper script also optionally performs HLA typing when HLA
+genes are included in the reference genome as additional ALT contigs.
 
 Other notable changes to BWA-MEM:
 
  * Added option `-b` to `bwa index`. This option tunes the batch size used in
    the construction of BWT. It is advised to use large `-b` for huge reference
-   sequences such as the *nt* database.
+   sequences such as the BLAST *nt* database.
 
- * Optimized for PacBio data. This includes a change to the scoring based on a
-   mini-study done by Aaron Quinlan and a heuristic speedup. Further speedup is
+ * Optimized for PacBio data. This includes a change to scoring based on a
+   study done by Aaron Quinlan and a heuristic speedup. Further speedup is
    possible, but needs more careful investigation.
 
- * Dropped PacBio read-to-read alignment for now. BWA-MEM is only good at
-   finding the best hit, not all hits. Option `-x pbread` is still available,
-   but hidden on the command line.
+ * Dropped PacBio read-to-read alignment for now. BWA-MEM is good for finding
+   the best hit, but is not very sensitive to suboptimal hits. Option `-x pbread`
+   is still available, but hidden on the command line. This may be removed in
+   future releases.
 
  * Added a new pre-setting for Oxford Nanopore 2D reads. LAST is still a little
-   more sensitive on bacterial data, but bwa-mem is times faster on human data.
+   more sensitive on older bacterial data, but bwa-mem is as good on more
+   recent data and is times faster for mapping against mammalian genomes.
 
  * Added LAST-like seeding. This improves the accuracy for longer reads.
 

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "18 November 2014" "bwa-0.7.11-r999" "Bioinformatics tools"
+.TH bwa 1 "21 December 2014" "bwa-0.7.11-r1032" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -75,7 +75,7 @@ appropriate algorithm will be chosen automatically.
 .TP
 .B mem
 .B bwa mem
-.RB [ -aCHMpP ]
+.RB [ -aCHjMpP ]
 .RB [ -t
 .IR nThreads ]
 .RB [ -k
@@ -88,6 +88,12 @@ appropriate algorithm will be chosen automatically.
 .IR seedSplitRatio ]
 .RB [ -c
 .IR maxOcc ]
+.RB [ -D
+.IR chainShadow ]
+.RB [ -m
+.IR maxMateSW ]
+.RB [ -W
+.IR minSeedMatch ]
 .RB [ -A
 .IR matchScore ]
 .RB [ -B
@@ -102,6 +108,8 @@ appropriate algorithm will be chosen automatically.
 .IR unpairPen ]
 .RB [ -R
 .IR RGline ]
+.RB [ -H
+.IR HDlines ]
 .RB [ -v
 .IR verboseLevel ]
 .I db.prefix
@@ -193,9 +201,28 @@ Discard a MEM if it has more than
 .I INT
 occurence in the genome. This is an insensitive parameter. [500]
 .TP
+.BI -D \ INT
+Drop chains shorter than
+.I FLOAT
+fraction of the longest overlapping chain [0.5]
+.TP
+.BI -m \ INT
+Perform at most
+.I INT
+rounds of mate-SW [50]
+.TP
+.BI -W \ INT
+Drop a chain if the number of bases in seeds is smaller than
+.IR INT .
+This option is primarily used for longer contigs/reads. When positive, it also
+affects seed filtering. [0]
+.TP
 .B -P
 In the paired-end mode, perform SW to rescue missing hits only but do not try to find
 hits that fit a proper pair.
+
+.TP
+.B SCORING OPTIONS:
 .TP
 .BI -A \ INT
 Matching score. [1]
@@ -244,15 +271,30 @@ and will be converted to a TAB in the output SAM. The read group ID will be
 attached to every read in the output. An example is '@RG\\tID:foo\\tSM:bar'.
 [null]
 .TP
+.BI -H \ ARG
+If ARG starts with @, it is interpreted as a string and gets inserted into the
+output SAM header; otherwise, ARG is interpreted as a file with all lines
+starting with @ in the file inserted into the SAM header. [null]
+.TP
 .BI -T \ INT
 Don't output alignment with score lower than
 .IR INT .
 This option affects output and occasionally SAM flag 2. [30]
 .TP
-.BI -h \ INT
+.BI -j
+Treat ALT contigs as part of the primary assembly (i.e. ignore the
+.I db.prefix.alt
+file).
+.TP
+.BI -h \ INT[,INT2]
 If a query has not more than
 .I INT
-hits with score higher than 80% of the best hit, output them all in the XA tag [5]
+hits with score higher than 80% of the best hit, output them all in the XA tag.
+If
+.I INT2
+is specified, BWA-MEM outputs up to
+.I INT2
+hits if the list contains a hit to an ALT contig. [5,200]
 .TP
 .B -a
 Output all found alignments for single-end or unpaired paired-end reads. These

fastmap.c

@@ -268,7 +268,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -p            smart pairing (ignoring in2.fq)\n");
 		fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
 		fprintf(stderr, "       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n");
-		fprintf(stderr, "       -j            ignore ALT contigs\n");
+		fprintf(stderr, "       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
 		fprintf(stderr, "       -T INT        minimum score to output [%d]\n", opt->T);