/***************************************************************************** # 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 "singleStrandedRegionsGotoList.h" #include "contig.h" #include "locatedFragment.h" #include "consedParameters.h" #include using namespace std; singleStrandedRegionsGotoList :: singleStrandedRegionsGotoList( Contig* pContig ) { int nPaddedLength = pContig->nGetDisplayableContigLength(); RWTValVector aPaddedContig( nPaddedLength ); for( int nZeroBased = 0; nZeroBased < nPaddedLength; ++nZeroBased ) aPaddedContig[ nZeroBased ] = 0; for( int nRead = 0; nRead < pContig->nGetNumberOfFragsInContig(); ++nRead ) { // get pointer to this located frag from contig LocatedFragment* pLocFrag = pContig->pLocatedFragmentGet( nRead ); // Phil said 980611 that: // > David: We *do* consider it covered by the unaligned part of a read if the // > user has turn off 'dim unaligned ends of read'. To be consistent, we // > should then say that in this case it is covered by a totally unaligned // > read. // Phil: No, this case is very different, since the read doesn't belong there at // all. (In the case where part of the read is aligned, the unaligned part is // still "covering" that region.) if (pLocFrag->bIsWholeReadUnaligned() ) continue; int nConsPosStart = pLocFrag->nGetAlignStart(); int nConsPosEnd = pLocFrag->nGetAlignEnd(); if ( !consedParameters::pGetConsedParameters()->bSearchFunctionsUseLowQualityEndsOfReads_ ) { if (pLocFrag->bIsWholeReadLowQuality() ) continue; // this read is no help nConsPosStart = pLocFrag->nGetHighQualityStart(); nConsPosEnd = pLocFrag->nGetHighQualityEnd(); } if ( !consedParameters::pGetConsedParameters()->bSearchFunctionsUseUnalignedEndsOfReads_ ) { if ( nConsPosStart < pLocFrag->nGetAlignClipStart() ) nConsPosStart = pLocFrag->nGetAlignClipStart(); if ( pLocFrag->nGetAlignClipEnd() < nConsPosEnd ) nConsPosEnd = pLocFrag->nGetAlignClipEnd(); } // what kind of a read is this unsigned char ucReadType = pLocFrag->ucGetReadType(); for( int nConsPos = nConsPosStart; nConsPos <= nConsPosEnd; ++nConsPos ) aPaddedContig[ nConsPos - pContig->nGetFirstDisplayableContigPos() ] |= ucReadType; } // for( int nRead = 0; ... // now find the single stranded segments int nStart; int nEnd; bool bWithinSingleStrandedRegion = false; for( int nConsPos = pContig->nGetStartConsensusIndex(); nConsPos <= pContig->nGetEndConsensusIndex(); ++nConsPos ) { Ntide nt = pContig->ntGetCons( nConsPos ); // ignore pads if ( nt.bIsPad() ) continue; unsigned char uc = aPaddedContig[ nConsPos - pContig->nGetFirstDisplayableContigPos() ]; bool bSingleStrandedAtThisBase = (uc == 0 ) || ( uc == 1 ) || ( uc == 2 ) || (uc == 4) || (uc == 8 ); if ( bSingleStrandedAtThisBase ) { // in single stranded region if (bWithinSingleStrandedRegion ) { // nEnd keeps growing with each base added nEnd = nConsPos; } else { // start a single stranded region bWithinSingleStrandedRegion = true; nStart = nConsPos; nEnd = nConsPos; } } else { if ( bWithinSingleStrandedRegion ) { // just finished a single stranded region char szLength[200]; sprintf( szLength, "%5d bp single strand/chem", nEnd - nStart + 1 ); RWCString soDescription( szLength ); gotoItem* pGotoItem = new gotoItem( pContig, NULL, // consensus location--not read nStart, nEnd, pContig->nUnpaddedIndex( nStart ), pContig->nUnpaddedIndex( nEnd ), soDescription ); bWithinSingleStrandedRegion = false; addToList( pGotoItem ); } } // if ( aPaddedContig ... else } // for( int nConsPos if ( bWithinSingleStrandedRegion ) { // just finished a single stranded region char szLength[200]; sprintf( szLength, "%5d bp single strand/chem", nEnd - nStart + 1 ); RWCString soDescription( szLength ); gotoItem* pGotoItem = new gotoItem( pContig, NULL, // consensus not read nStart, nEnd, pContig->nUnpaddedIndex( nStart ), pContig->nUnpaddedIndex( nEnd ), soDescription ); addToList( pGotoItem ); } }