Release 0.7.16-r1180

NEWS.md

@@ -1,7 +1,24 @@
+Release 0.7.16 (30 July 2017)
+-----------------------------
+
+This release added a couple of minor features and incorporated multiple pull
+requests, including:
+
+ * Added option -5, which is useful to some Hi-C pipelines.
+
+ * Fixed an error with samtools sorting (#129). Updated download link for
+   GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple
+   issues via a collected pull request #139 by @jmarshall. Avoid malformatted
+   SAM header when -R is used with TAB (#84). Output mate CIGAR (#138).
+
+(0.7.16: 30 July 2017, r1180)
+
+
+
 Release 0.7.15 (31 May 2016)
 ----------------------------
 
-Fixed a long existing bug which potentially leads underestimated insert size
+Fixed a long existing bug which potentially leads to underestimated insert size
 upper bound. This bug should have little effect in practice.
 
 (0.7.15: 31 May 2016, r1140)

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "31 May 2016" "bwa-0.7.15-r1140" "Bioinformatics tools"
+.TH bwa 1 "30 July 2017" "bwa-0.7.16-r1180" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -261,16 +261,20 @@ more aggressive read pair. [17]
 .TP
 .BI -x \ STR
 Read type. Changes multiple parameters unless overriden [null]
-    pacbio:
+.RS
+.TP 10
+.BR pacbio :
 .B -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0
 (PacBio reads to ref)
-    ont2d:
+.TP
+.BR ont2d :
 .B -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0
 (Oxford Nanopore 2D-reads to ref)
-    intractg:
+.TP
+.BR intractg :
 .B -B9 -O16 -L5
 (intra-species contigs to ref)
-
+.RE
 .TP
 .B INPUT/OUTPUT OPTIONS:
 .TP
@@ -299,6 +303,21 @@ For compatibility with other BWA commands, this option may also be given as
 .IR FILE .
 [standard ouptut]
 .TP
+.B -5
+For split alignment, mark the segment with the smallest coordinate as the
+primary. This option may help some Hi-C pipelines. By default, BWA-MEM marks
+highest scoring segment as primary.
+.TP
+.B -K \ INT
+Process
+.I INT
+input bases in each batch regardless of the number of threads in use
+.RI [10000000* nThreads ].
+By default, the batch size is proportional to the number of threads in use.
+Because the inferred insert size distribution slightly depends on the batch
+size, using different number of threads may produce different output.
+Specifying this option helps reproducibility.
+.TP
 .BI -T \ INT
 Don't output alignment with score lower than
 .IR INT .

fastmap.c

@@ -268,9 +268,10 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n");
 		fprintf(stderr, "       -o FILE       sam file to output results to [stdout]\n");
 		fprintf(stderr, "       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
-		fprintf(stderr, "       -5            always take the leftmost alignment on a read as primary\n");
+		fprintf(stderr, "       -5            for split alignment, take the alignment with the smallest coordiate as primary\n");
+		fprintf(stderr, "       -K INT        process INT input bases in each batch regardless of nThreads (for reproducibility) []\n");
 		fprintf(stderr, "\n");
-		fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
+		fprintf(stderr, "       -v INT        verbosity 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);
 		fprintf(stderr, "       -h INT[,INT]  if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
 		fprintf(stderr, "       -a            output all alignments for SE or unpaired PE\n");

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.15-r1144-dirty"
+#define PACKAGE_VERSION "0.7.16-r1180"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);