r340: feature freeze; updated the manpage

I will stop adding new features to bwa and prepare for the next release. I will
briefly evaluate the variant calling accuracy before the release.

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "27 Feburary 2013" "bwa-0.7.0" "Bioinformatics tools"
+.TH bwa 1 "10 March 2013" "bwa-0.7.1" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -81,6 +81,8 @@ genome.
 .IR minSeedLen ]
 .RB [ -w
 .IR bandWidth ]
+.RB [ -d
+.IR zDropoff ]
 .RB [ -r
 .IR seedSplitRatio ]
 .RB [ -c
@@ -163,6 +165,21 @@ Band width. Essentially, gaps longer than
 will not be found. Note that the maximum gap length is also affected by the
 scoring matrix and the hit length, not solely determined by this option. [100]
 .TP
+.BI -d \ INT
+Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between
+the best and the current extension score is above
+.RI | i - j |* A + INT ,
+where
+.I i
+and
+.I j
+are the current positions of the query and reference, respectively, and
+.I A
+is the matching score. Z-dropoff is similar to BLAST's X-dropoff except that it
+doesn't penalize gaps in one of the sequences in the alignment. Z-dropoff not
+only avoids unnecessary extension, but also reduces poor alignments inside a
+long good alignment. [100]
+.TP
 .BI -r \ FLOAT
 Trigger re-seeding for a MEM longer than
 .IR minSeedLen * FLOAT .
@@ -215,6 +232,11 @@ 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 -T \ INT
+Don't output alignment with score lower than
+.IR INT .
+This option only affects output. [30]
+.TP
 .B -a
 Output all found alignments for single-end or unpaired paired-end reads. These
 alignments will be flagged as secondary alignments.

fastmap.c

@@ -59,7 +59,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -t INT     number of threads [%d]\n", opt->n_threads);
 		fprintf(stderr, "       -k INT     minimum seed length [%d]\n", opt->min_seed_len);
 		fprintf(stderr, "       -w INT     band width for banded alignment [%d]\n", opt->w);
-		fprintf(stderr, "       -d INT     off-diagnal X-dropoff [%d]\n", opt->zdrop);
+		fprintf(stderr, "       -d INT     off-diagonal X-dropoff [%d]\n", opt->zdrop);
 		fprintf(stderr, "       -r FLOAT   look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
 //		fprintf(stderr, "       -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "       -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);

main.c

@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r339-beta"
+#define PACKAGE_VERSION "0.7.0-r340-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);
@@ -34,7 +34,7 @@ static int usage()
 	fprintf(stderr, "Command: index         index sequences in the FASTA format\n");
 	fprintf(stderr, "         mem           BWA-MEM algorithm\n");
 	fprintf(stderr, "         fastmap       identify super-maximal exact matches\n");
-	fprintf(stderr, "         pemerge       merge overlapping paired ends\n");
+	fprintf(stderr, "         pemerge       merge overlapping paired ends (EXPERIMENTAL)\n");
 	fprintf(stderr, "         aln           gapped/ungapped alignment\n");
 	fprintf(stderr, "         samse         generate alignment (single ended)\n");
 	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");