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read_sam
read_sam read in alignment entries from SAM files.
Currently only single end alignments can be parsed.
The resulting Biopiece record consists of the following record type:
MAPQ: 37
STRAND: -
Q_ID: ID00016152
ALIGN: 65:G>-
S_ID: gi|48994873|gb|U00096.2|
REC_TYPE: SAM
S_BEG: 7436
SEQ: TCAAAAGAAAAACTCAGGGCGCGGGCAACGGCGTTCGCTTGAACTCCGCTGAAAATTATGCCATAGCGATGAGCAAAAAGACGGCGAACAGAACGCCCAT
CIGAR: 65M1D35M
---
The ALIGN field that holds the alignment descriptors as described in the KISS format specifications:
http://code.google.com/p/biopieces/wiki/KissFormat
For more about the SAM format:
http://samtools.sourceforge.net/SAM1.pdf
read_sam [options] -i <SAM file(s)>
[-? | --help] # Print full usage description.
[-i <files!> | --data_in=<files!>] # Comma separated list of files or glob expression to read.
[-n <uint> | --num=<uint>] # Limit number of records to read.
[-e <string> | --encoding=<string>] # Encoding <auto|base_33|base_64> - Default=auto
[-I <file> | --stream_in=<file!>] # Read input stream from file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
To read all SAM entries from a file:
read_sam -i test.sam
To read in only 10 records from a SAM file:
read_sam -n 10 -i test.sam
To read all SAM entries from multiple files:
read_sam -i test1.sam,test2.sam
To read SAM entries from multiple files using a glob expression:
read_sam -i '*.sam'
Martin Asser Hansen - Copyright (C) - All rights reserved.
October 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_sam is part of the Biopieces framework.