Incorporate patches by Marcel Martin for read counting.

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 09cb14765df6cde33503e9eebd4a84577edd4f6c..7de9857245ca6debe24abaa4d6786f942886035e 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -47,7 +47,7 @@ entire alignment file unless it is asked to do so.
 
 .TP 10
 .B view
-samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
 skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]
 
 Extract/print all or sub alignments in SAM or BAM format. If no region
@@ -100,6 +100,15 @@ Input is in SAM. If @SQ header lines are absent, the
 .B `-t'
 option is required.
 .TP
+.B -c
+Instead of printing the alignments, only count them and print the
+total number. All filter options, such as
+.B `-f',
+.B `-F'
+and
+.B `-q'
+, are taken into account.
+.TP
 .BI -t " FILE"
 This file is TAB-delimited. Each line must contain the reference name
 and the length of the reference, one line for each distinct reference;