diff --git a/doc/samtools.1 b/doc/samtools.1 index 28669ef03..b367174d5 100644 --- a/doc/samtools.1 +++ b/doc/samtools.1 @@ -937,11 +937,47 @@ block compression. CRAM output only; defaults to 0 (off). Permits use of lzma in CRAM block compression. .TP +.BI use_fqz= 0|1 +CRAM \(>= 3.1 output only; enables and disables the fqzcomp quality +compression method. This is on by default for version 3.1 and above +only when the small and archive profiles are in use. +.TP +.BI use_tok= 0|1 +CRAM \(>= 3.1 output only; enables and disables the namne tokeniser +compression method. This is on by default for version 3.1 and above. +.TP .BI lossy_names= 0|1 CRAM output only; defaults to 0 (off). If 1, templates with all members within the same CRAM slice will have their read names removed. New names will be automatically generated during decoding. Also see the \fBname_prefix\fR option. +.TP +.B fast, normal, small, archive +CRAM output only. Set the CRAM compression profile. This is a +simplified way of setting many output options at once. It changes the +following options according to the profile in use. The "normal" +profile is the default. + +.TS +lb l l l l . +Option \fBfast\fR \fBnormal\fR \fBsmall\fR \fBarchive\fR +level 1 5 6 7 +use_bzip2 off off on on +use_lzma off off off on if level>7 +use_tok(*) off on on on +use_fqz(*) off off on on +use_arith(*) off off off on +seqs_per_slice 10000 10000 25000 100000 +.TE + +(*) \fBuse_tok\fR, \fBuse_fqz\fR and \fBuse_arith\fR are only +enabled for CRAM version 3.1 and above. + +The \fBlevel\fR listed is only the default value, and will not be set +if it has been explicitly changed already. Additionally +\fBbases_per_slice\fR is set to \fB500*seqs_per_slice\fR unless previously +explicitly set. + .RE .PP For example: @@ -949,6 +985,8 @@ For example: samtools view --input-fmt-option decode_md=0 --output-fmt cram,version=3.0 --output-fmt-option embed_ref --output-fmt-option seqs_per_slice=2000 -o foo.cram foo.bam + +samtools view -O cram,small -o bar.cram bar.bam .EE .PP The \fB--write-index\fR option enables automatic index creation while