[med-svn] [bwa] 01/05: Imported Upstream version 0.7.15

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit 9b4cfaa2ec63015ae943cb8e1470da06a7d92021
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 3 17:26:16 2016 +0200

    Imported Upstream version 0.7.15
---
 NEWS.md           | 20 ++++++++++++++++++++
 bwa.1             |  4 ++--
 bwa.c             |  7 +++++--
 bwakit/run-bwamem |  4 ++--
 bwamem_pair.c     |  2 +-
 bwtsw2_pair.c     |  2 +-
 main.c            |  2 +-
 7 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 15c2762..9a63bef 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,23 @@
+Release 0.7.15 (31 May 2016)
+----------------------------
+
+Fixed a long existing bug which potentially leads underestimated insert size
+upper bound. This bug should have little effect in practice.
+
+(0.7.15: 31 May 2016, r1140)
+
+
+
+Release 0.7.14 (4 May 2016)
+---------------------------
+
+In the ALT mapping mode, this release adds the "AH:*" header tag to SQ lines
+corresponding to alternate haplotypes.
+
+(0.7.14: 4 May 2016, r1136)
+
+
+
 Release 0.7.13 (23 Feburary 2016)
 ---------------------------------
 
diff --git a/bwa.1 b/bwa.1
index 994f96a..b9a65f1 100644
--- a/bwa.1
+++ b/bwa.1
@@ -1,4 +1,4 @@
-.TH bwa 1 "23 December 2014" "bwa-0.7.12-r1034" "Bioinformatics tools"
+.TH bwa 1 "31 May 2016" "bwa-0.7.15-r1140" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -202,7 +202,7 @@ Discard a MEM if it has more than
 .I INT
 occurence in the genome. This is an insensitive parameter. [500]
 .TP
-.BI -D \ INT
+.BI -D \ FLOAT
 Drop chains shorter than
 .I FLOAT
 fraction of the longest overlapping chain [0.5]
diff --git a/bwa.c b/bwa.c
index f9ce6a1..c78ebb6 100644
--- a/bwa.c
+++ b/bwa.c
@@ -379,8 +379,11 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
 		}
 	}
 	if (n_SQ == 0) {
-		for (i = 0; i < bns->n_seqs; ++i)
-			err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
+		for (i = 0; i < bns->n_seqs; ++i) {
+			err_printf("@SQ\tSN:%s\tLN:%d", bns->anns[i].name, bns->anns[i].len);
+			if (bns->anns[i].is_alt) err_printf("\tAH:*\n");
+			else err_fputc('\n', stdout);
+		}
 	} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
 		fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
 	if (hdr_line) err_printf("%s\n", hdr_line);
diff --git a/bwakit/run-bwamem b/bwakit/run-bwamem
index 165f93e..462bafe 100755
--- a/bwakit/run-bwamem
+++ b/bwakit/run-bwamem
@@ -5,7 +5,7 @@ use warnings;
 use Getopt::Std;
 
 my %opts = (t=>1);
-getopts("SadskHo:R:x:t:", \%opts);
+getopts("PSadskHo:R:x:t:", \%opts);
 
 die('
 Usage:   run-bwamem [options] <idxbase> <file1> [file2]
@@ -151,7 +151,7 @@ $cmd .= "  | $root/bwa mem $bwa_opts$ARGV[0] - 2> $prefix.log.bwamem \\\n";
 $cmd .= "  | $root/samblaster 2> $prefix.log.dedup \\\n" if defined($opts{d});
 
 my $has_hla = 0;
-if (-f "$ARGV[0].alt") {
+if (-f "$ARGV[0].alt" && !defined($opts{P})) {
 	my $fh;
 	open($fh, "$ARGV[0].alt") || die;
 	while (<$fh>) {
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 7950736..b812cc0 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -94,7 +94,7 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
 		r->low  = (int)(p25 - MAPPING_BOUND * (p75 - p25) + .499);
 		r->high = (int)(p75 + MAPPING_BOUND * (p75 - p25) + .499);
 		if (r->low  > r->avg - MAX_STDDEV * r->std) r->low  = (int)(r->avg - MAX_STDDEV * r->std + .499);
-		if (r->high < r->avg - MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
+		if (r->high < r->avg + MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
 		if (r->low < 1) r->low = 1;
 		fprintf(stderr, "[M::%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r->low, r->high);
 		free(q->a);
diff --git a/bwtsw2_pair.c b/bwtsw2_pair.c
index 24905df..b945128 100644
--- a/bwtsw2_pair.c
+++ b/bwtsw2_pair.c
@@ -82,7 +82,7 @@ bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
 	r.high = (int)(p75 + 3. * (p75 - p25) + .499);
 	if (r.low > r.avg - MAX_STDDEV * r.std) r.low = (int)(r.avg - MAX_STDDEV * r.std + .499);
 	r.low = tmp > max_len? tmp : max_len;
-	if (r.high < r.avg - MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
+	if (r.high < r.avg + MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
 	ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
 	free(isize);
 	return r;
diff --git a/main.c b/main.c
index a5ae5fa..f936a81 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.13-r1126"
+#define PACKAGE_VERSION "0.7.15-r1140"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);

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