source: trunk/yat/utility/Cigar.h @ 3306

#ifndef theplu_yat_utility_cigar
#define theplu_yat_utility_cigar

// $Id: Cigar.h 3306 2014-08-21 04:37:21Z peter $

/*
  Copyright (C) 2014 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program. If not, see <http://www.gnu.org/licenses/>.
*/

// This file defines some PP macro for CIGAR


#include "config_public.h"

// allow inclusion of config_bam.h so this file is available also without bam.h
#ifdef YAT_HAVE_LIBBAM
#include "yat/omic/config_bam.h"
#include YAT_BAM_HEADER
#else // if bam.h is not available #define CIGAR
/// describe how CIGAR operation/length is packed into a 32-bit
#define BAM_CIGAR_SHIFT 4
/// operation is described in four lowest bits
#define BAM_CIGAR_MASK  ((1 << BAM_CIGAR_SHIFT) - 1)
/// \abstract CIGAR: M = match or mismatch
#define BAM_CMATCH      0
/// \abstract CIGAR: I = insertion to the reference
#define BAM_CINS        1
/// \abstract CIGAR: D = deletion from the reference
#define BAM_CDEL        2
/// \abstract CIGAR: N = skip on the reference (e.g. spliced alignment)
#define BAM_CREF_SKIP   3
/// \abstract CIGAR: S = clip on the read with clipped sequence
/// present in qseq
#define BAM_CSOFT_CLIP  4
/// \abstract CIGAR: H = clip on the read with clipped sequence trimmed off
#define BAM_CHARD_CLIP  5
/// \abstract CIGAR: P = padding
#define BAM_CPAD        6
/// \abstract CIGAR: equals = match
#define BAM_CEQUAL      7
/// \abstract CIGAR: X = mismatch
#define BAM_CDIFF       8
#endif // end of YAT_HAVE_LIBBAM

// BAM_CBACK is not defined in old versions of bam.h
#ifndef BAM_CBACK
#define BAM_CBACK 9
#endif

// backport #defines from samtools 0.1.19
#ifndef BAM_CIGAR_STR
#define BAM_CIGAR_STR "MIDNSHP=XB"
// lookup table used in bam_cigar_type
#define BAM_CIGAR_TYPE 0x3C1A7

/// index of operation in range [0, 9], see below.
#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
// length of the operation
#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
// char describing the operation, see column 2 in table below
#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
// Create a cigar element with length l and operation o
#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
// Returns a two-bits number describing the type of operation. The
// first bit, bam_cigar_type & 1, (4th column in table below) is 1 iff
// operation consumes query sequence. The second bit, bam_cigar_type &
// 2, (3rd column below) is 1 iff operation consumes reference
// sequence.
#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3)
#endif // end of backport

#endif // end of file