fine tune the wrapper scripts

NEWS.md

@@ -9,9 +9,9 @@ mapping, we start to provide a wrapper script and precompiled binaries since
 this release. Please check README-alt.md for details.
 
 Another major addition to BWA-MEM is HLA typing, which made possible with the
-new ALT mapping strategy. Necessary data and programs are also included in
-the binary release. The wrapper script also performs HLA typing when HLA genes
-are also included in the reference genome as additional ALT contigs.
+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
+also included in the reference genome as additional ALT contigs.
 
 Other notable changes to BWA-MEM:
 

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "19 May 2014" "bwa-0.7.9-r783" "Bioinformatics tools"
+.TH bwa 1 "18 November 2014" "bwa-0.7.11-r999" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -233,8 +233,9 @@ more aggressive read pair. [17]
 .B INPUT/OUTPUT OPTIONS:
 .TP
 .B -p
-Assume the first input query file is interleaved paired-end FASTA/Q. See the
-command description for details.
+Smart pairing. If two adjacent reads have the same name, they are considered
+to form a read pair. This way, paired-end and single-end reads can be mixed
+in a single FASTA/Q stream.
 .TP
 .BI -R \ STR
 Complete read group header line. '\\t' can be used in

extras/run-bwamem

@@ -4,8 +4,8 @@ use strict;
 use warnings;
 use Getopt::Std;
 
-my %opts = (t=>1, n=>64);
-getopts("Sadsko:R:x:t:", \%opts);
+my %opts = (t=>1);
+getopts("SadskHo:R:x:t:", \%opts);
 
 die('
 Usage:   run-bwamem [options] <idxbase> <file1> [file2]
@@ -22,6 +22,7 @@ Options: -o STR    prefix for output files                       [inferred from
          -d        mark duplicate (via samblaster)
          -S        for SAM/BAM input, don\'t shuffle
          -s        sort the output alignment (requring more RAM)
+         -H        skip HLA typing
          -k        keep temporary files generated by typeHLA
 
 Examples:
@@ -31,15 +32,15 @@ Examples:
      run-bwamem -o prefix -t8 -R"@RG\tID:foo\tSM:bar" hs38d6.fa read1.fq.gz read2.fq.gz
 
  * Remap coordinate-sorted BAM, trim Illumina PE adapters and sort the output. The BAM
-   may contain single-end or paired-end reads, or a mixture of the two types. The read
-   groups are not transferred to the output BAM.
+   may contain single-end or paired-end reads, or a mixture of the two types. Read groups
+   are not transferred to the output BAM, though.
 
      run-bwamem -sao prefix hs38d6.fa old-srt.bam
 
  * Remap name-grouped BAM and mark duplicates. Note that in this case, all reads from
    a single library should be aligned at the same time. Paired-end only.
 
-	 run-bwamem -Sdo prefix hs38d6.fa old-unsrt.bam
+      run-bwamem -Sdo prefix hs38d6.fa old-unsrt.bam
 
 Output files:
 
@@ -119,7 +120,7 @@ if ($is_sam || $is_bam) {
 
 my $bwa_opts = "-p " . ($opts{t} > 1? "-t$opts{t} " : "") . (defined($opts{x})? "-x $opts{x} " : "") . (defined($opts{R})? "-R'$opts{R}' " : "");
 
-$cmd .= "  | $root/trimadap \\\n" if defined($opts{a});
+$cmd .= "  | $root/trimadap 2> $prefix.log.trim \\\n" if defined($opts{a});
 $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});
 
@@ -138,8 +139,8 @@ if (-f "$ARGV[0].alt") {
 my $t_sort = $opts{t} < 4? $opts{t} : 4;
 $cmd .= defined($opts{s})? "  | $root/samtools sort -@ $t_sort -m1G - $prefix.aln;\n" : "  | $root/samtools view -1 - > $prefix.aln.bam;\n";
 
-if ($has_hla && (!defined($opts{x}) || $opts{x} eq 'intractg')) {
-	$cmd .= "$root/run-HLA ". ($opts{x} eq 'intractg'? "-A " : "") . "$prefix.hla > $prefix.hla.top 2> $prefix.log.hla;\n";
+if ($has_hla && !defined($opts{H}) && (!defined($opts{x}) || $opts{x} eq 'intractg')) {
+	$cmd .= "$root/run-HLA ". (defined($opts{x}) && $opts{x} eq 'intractg'? "-A " : "") . "$prefix.hla > $prefix.hla.top 2> $prefix.log.hla;\n";
 	$cmd .= "cat $prefix.hla.HLA*.gt | grep ^GT | cut -f2- > $prefix.hla.all;\n";
 	$cmd .= "rm -f $prefix.hla.HLA*;\n" unless defined($opts{k});
 }

extras/typeHLA.sh

@@ -20,7 +20,7 @@ if [ $is_ctg -eq 0 ]; then
 	echo "** De novo assembling..." >&2
 	len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
 	$root/fermi2.pl unitig -f $root/fermi2 -r $root/ropebwt2 -t2 -l$len -p $pre.tmp $pre.fq > $pre.tmp.mak
-	make -f $pre.tmp.mak
+	make -f $pre.tmp.mak >&2
 	cp $pre.tmp.mag.gz $pre.mag.gz
 else
 	rm -f $pre.tmp.mag.gz