diff --git a/NEWS.md b/NEWS.md index 9a63bef..02a1c0c 100644 --- a/NEWS.md +++ b/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) diff --git a/bwa.1 b/bwa.1 index da158d8..94c2c58 100644 --- a/bwa.1 +++ b/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 . diff --git a/fastmap.c b/fastmap.c index 0619999..d89c495 100644 --- a/fastmap.c +++ b/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 .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 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"); diff --git a/main.c b/main.c index a0f25fa..21bff9b 100644 --- a/main.c +++ b/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[]);