/***************************************************************************** # 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(); }