/*****************************************************************************
# Copyright (C) 1994-2008 by David Gordon.
# All rights reserved.
#
# This software is part of a beta-test version of the Consed/Autofinish
# package. It should not be redistributed or
# used for any commercial purpose, including commercially funded
# sequencing, without written permission from the author and the
# University of Washington.
#
# This software is provided ``AS IS'' and any express or implied
# warranties, including, but not limited to, the implied warranties of
# merchantability and fitness for a particular purpose, are disclaimed.
# In no event shall the authors or the University of Washington be
# liable for any direct, indirect, incidental, special, exemplary, or
# consequential damages (including, but not limited to, procurement of
# substitute goods or services; loss of use, data, or profits; or
# business interruption) however caused and on any theory of liability,
# whether in contract, strict liability, or tort (including negligence
# or otherwise) arising in any way out of the use of this software, even
# if advised of the possibility of such damage.
#
# Building Consed from source is error prone and not simple which is
# why I provide executables. Due to time limitations I cannot
# provide any assistance in building Consed. Even if you do not
# modify the source, you may introduce errors due to using a
# different version of the compiler, a different version of motif,
# different versions of other libraries than I used, etc. For this
# reason, if you discover Consed bugs, I can only offer help with
# those bugs if you first reproduce those bugs with an executable
# provided by me--not an executable you have built.
#
# Modifying Consed is also difficult. Although Consed is modular,
# some modules are used by many other modules. Thus making a change
# in one place can have unforeseen effects on many other features.
# It may takes months for you to notice these other side-effects
# which may not seen connected at all. It is not feasable for me to
# provide help with modifying Consed sources because of the
# potentially huge amount of time involved.
#
#*****************************************************************************/
#include "sysdepend.h"
#include "highQualityDiscrepancyGotoList.h"
#include "quality.h"
#include "contig.h"
#include "locatedFragment.h"
#include "consedParameters.h"
#include "assert.h"
static char* szGotoItemDesc = "high quality base disagrees with consensus";
// ctor reads through consensus of passed contig, adds a
// gotoItem to list each time it encounters a region where
// quality is <= qualityLow (as defined by quality.h)
highQualityDiscrepancyGotoList :: highQualityDiscrepancyGotoList(
Contig* pContig,
const bool bExcludeCompressionOrG_dropoutTags,
const bool bExcludeSpuriousPads )
{
Contig* pOldContig = NULL;
LocatedFragment* pOldLocFrag = NULL;
int nOldConsPos = 0;
gotoItem* pOldGotoItem = NULL;
int nQualityThreshold =
consedParameters::pGetConsedParameters()->nQualityThresholdForFindingHighQualityDiscrepancies_;
int nNumFrags = pContig->nGetNumberOfFragsInContig();
for (int nFrag = 0; nFrag < nNumFrags; nFrag++) {
// get pointer to this located frag from contig
LocatedFragment* pLocFrag = pContig->pLocatedFragmentGet(nFrag);
for( int nConsPos = pLocFrag->nGetAlignStart();
nConsPos <= pLocFrag->nGetAlignEnd();
++nConsPos ) {
if ( (pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality() >=
nQualityThreshold) &&
(pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality() !=
ucQualityLowEdited) ) {
if (
(
pLocFrag->ntGetFragFromConsPos( nConsPos ).cGetBase() !=
pContig->cGetConsensusBase( nConsPos )
)
// Phil said to allow pads as highQualityDiscrepancies
// on Nov 26, 1997
// &&
// !pLocFrag->ntGetFragFromConsPos( nConsPos ).bIsPad()
) {
// Phil decided Dec 27, 1997 to only show high quality
// discrepancies if in the aligned part of the read
if ( !pLocFrag->bIsInAlignedPartOfRead( nConsPos ) )
continue;
if ( nConsPos <
( pLocFrag->nGetAlignClipStart() +
consedParameters::pGetConsedParameters()->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ) )
continue;
if ( ( pLocFrag->nGetAlignClipEnd() -
consedParameters::pGetConsedParameters()->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ )
< nConsPos )
continue;
if ( bExcludeCompressionOrG_dropoutTags ) {
if ( pLocFrag->bIsWithinACompressionOrG_dropoutTag( nConsPos ) )
continue;
}
if ( bExcludeSpuriousPads ) {
if ( pLocFrag->ntGetFragFromConsPos( nConsPos ).cGetBase()
== '*' ) {
// the high quality discrepancy is a pad. Let's see
// what the consensus has here and if it is a repeated base.
// If it is a possible misassembly, then show it in the
// hqd list. If it is a spurious hqd pad, do not show
// it.
if ( !pContig->bDoesPadIndicateAPossibleMisassemblyHere(
pLocFrag,
nConsPos ) ) {
// these are the hqd's that would be eliminated from
// the hqd list
continue;
}
}
}
if ( (pOldContig == pContig) &&
(pOldLocFrag == pLocFrag) &&
( ( nOldConsPos + 1) == nConsPos ) ) {
pOldGotoItem->setNewEnd( nConsPos,
pContig->nUnpaddedIndex( nConsPos ) );
nOldConsPos = nConsPos;
}
else {
gotoItem* pGotoItem =
new gotoItem(
pContig,
pLocFrag,
nConsPos, // start padded
nConsPos, // end padded
pContig->nUnpaddedIndex( nConsPos ),// start unpadded
pContig->nUnpaddedIndex( nConsPos ), // end unpadded
szGotoItemDesc,
true, // bPrefixContigToDescription
NULL ); // pOtherData
addToList(pGotoItem);
pOldGotoItem = pGotoItem;
pOldContig = pContig;
pOldLocFrag = pLocFrag;
nOldConsPos = nConsPos;
}
}
}
}
}
sortByPosition();
} // highQualityDiscrepancyGotoList