/*****************************************************************************
# 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 "editedButNotNsGotoList.h"
#include "quality.h"
#include "contig.h"
#include "locatedFragment.h"
#include "consedParameters.h"
static char* szGotoItemDesc = "edited bases that aren't N's";
editedButNotNsGotoList :: editedButNotNsGotoList(Contig* pContig)
{
Contig* pOldContig = NULL;
LocatedFragment* pOldLocFrag = NULL;
int nOldConsPos = 0;
gotoItem* pOldGotoItem = NULL;
int nNumFrags = pContig->nGetNumberOfFragsInContig();
int nFrag;
for( 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() ==
ucQualityHighEdited )
||
(pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality() ==
ucQualityLowEdited ) ) {
if (pLocFrag->ntGetFragFromConsPos( nConsPos ).cGetBase() != 'n' ) {
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);
addToList(pGotoItem);
pOldGotoItem = pGotoItem;
pOldContig = pContig;
pOldLocFrag = pLocFrag;
nOldConsPos = nConsPos;
}
}
} // if (pLocFrag->ntGetFragFromConsPos( nConsPos ).cGetBase() != 'n'
} // if ( (pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality(...
} // for (int nFrag = 0; nFrag < nNumFrags; nFrag++) {
// now checking for deleted bases--these bases can be
// found because they have edit tags attached to them.
// However, we don't want to duplicate items that have
// already been found above, hence the check that the
// bases are not quality 98 or 99
for (nFrag = 0; nFrag < nNumFrags; nFrag++) {
// get pointer to this located frag from contig
LocatedFragment* pLocFrag = pContig->pLocatedFragmentGet(nFrag);
int nNumberOfTags = pLocFrag->nGetNumberOfTags();
for( int nTag = 0; nTag < nNumberOfTags; ++nTag ) {
tag* pTag = pLocFrag->pGetTag( nTag );
if ( pTag->soGetTagType() == "edit" ) {
// check if any of the bases are not 98 or 99
int nGotoStart;
int nGotoEnd;
bool bStartedGotoItem = false;
for( int nConsPos = pTag->nPaddedConsPosStart_;
nConsPos <= pTag->nPaddedConsPosEnd_;
++nConsPos ) {
if (pLocFrag->ntGetFragFromConsPos( nConsPos ).cGetBase() == 'n' )
continue;
Quality qual =
pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality();
if (
( qual != ucQualityLowEdited ) &&
( qual != ucQualityHighEdited )
) {
// how this base is not in the list above
// So now we have a edited position to add to the list
if ( !bStartedGotoItem ) {
bStartedGotoItem = true;
nGotoStart = nConsPos;
nGotoEnd = nConsPos;
}
else {
nGotoEnd = nConsPos;
}
}
} // for( int nConsPos ...
if ( bStartedGotoItem ) {
gotoItem* pGotoItem = new gotoItem(pContig,
pLocFrag,
nGotoStart, // start padded
nGotoEnd, // end padded
pContig->nUnpaddedIndex( nGotoStart ),// start unpadded
pContig->nUnpaddedIndex( nGotoEnd ), // end unpadded
szGotoItemDesc);
addToList(pGotoItem);
}
} // if ( pTag->soGetTagType() == "edit" )
}
}
// sort by consensus position
sortByPosition();
}