[med-svn] [Git][med-team/chromhmm][master] 5 commits: Fix clean target
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Feb 7 07:19:25 GMT 2024
Andreas Tille pushed to branch master at Debian Med / chromhmm
Commits:
579240f2 by Andreas Tille at 2024-02-07T08:13:07+01:00
Fix clean target
- - - - -
91d4109c by Andreas Tille at 2024-02-07T08:14:29+01:00
routine-update: New upstream version
- - - - -
b4fbc486 by Andreas Tille at 2024-02-07T08:14:30+01:00
New upstream version 1.25+dfsg
- - - - -
c9085fab by Andreas Tille at 2024-02-07T08:14:40+01:00
Update upstream source from tag 'upstream/1.25+dfsg'
Update to upstream version '1.25+dfsg'
with Debian dir f1610bcb8039f161f0c03302f99ab137b19666b0
- - - - -
b6f2ef79 by Andreas Tille at 2024-02-07T08:16:26+01:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- + LICENSE
- debian/changelog
- + debian/clean
- debian/control
- edu/mit/compbio/ChromHMM/BrowserOutput.java
- edu/mit/compbio/ChromHMM/ChromHMM.java
- edu/mit/compbio/ChromHMM/ConvertGeneTable.java
- versionlog.txt
Changes:
=====================================
LICENSE
=====================================
@@ -0,0 +1,674 @@
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+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program 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.
+
+ This program 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 <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+chromhmm (1.25+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * Fix clean target
+ Closes: #1043980
+ Use secure URI in Homepage field.
+ Replace XC-Package-Type with Package-Type.
+ Remove unnecessary XS-Testsuite field in debian/control.
+
+ -- Andreas Tille <tille at debian.org> Wed, 07 Feb 2024 08:15:09 +0100
+
chromhmm (1.24+dfsg-1) unstable; urgency=medium
* Team Upload.
=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+chromhmm.jar
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends-Indep: default-jdk
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/chromhmm
Vcs-Git: https://salsa.debian.org/med-team/chromhmm.git
-Homepage: http://compbio.mit.edu/ChromHMM/
+Homepage: https://compbio.mit.edu/ChromHMM/
Rules-Requires-Root: no
Package: chromhmm
=====================================
edu/mit/compbio/ChromHMM/BrowserOutput.java
=====================================
@@ -125,9 +125,13 @@ public class BrowserOutput
*/
boolean bgzip;
+ /**
+ * True if header leaders on browser bed files should be surpressed
+ */
+ boolean bnobrowserheader;
public BrowserOutput(String szsegmentfile, String szcolormapping,String szidlabelmapping,
- String szsegmentationname, String szoutputfileprefix, int numstates, boolean bgzip) throws IOException
+ String szsegmentationname, String szoutputfileprefix, int numstates, boolean bgzip, boolean bnobrowserheader) throws IOException
{
this.szsegmentfile = szsegmentfile;
this.szcolormapping =szcolormapping;
@@ -136,6 +140,7 @@ public class BrowserOutput
this.szoutputfileprefix = szoutputfileprefix;
this.numstates = numstates;
this.bgzip = bgzip;
+ this.bnobrowserheader = bnobrowserheader;
hmcolor = new HashMap();
hmlabelExtend = new HashMap();
@@ -383,7 +388,7 @@ public class BrowserOutput
int nend = Integer.parseInt(st.nextToken().trim());
String szFullID = st.nextToken().trim();
String szID = szFullID.substring(1); //this removes ordering type
- if (bfirst)
+ if ((bfirst)&&(!bnobrowserheader))
{
String szout = "track name=\""+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szFullID.charAt(0))
+" ordered)"+"\" visibility=1 itemRgb=\"On\""+"\n";
@@ -423,7 +428,7 @@ public class BrowserOutput
String szLine;
boolean bfirst = true;
- while ((szLine =brsegment.readLine())!=null)
+ while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szcurrchrom = st.nextToken().trim();
@@ -431,7 +436,7 @@ public class BrowserOutput
int nend = Integer.parseInt(st.nextToken().trim());
String szFullID = st.nextToken().trim();
String szID = szFullID.substring(1); //this removes ordering type
- if (bfirst)
+ if ((bfirst)&&(!bnobrowserheader))
{
pw.println("track name=\""+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szFullID.charAt(0))
+" ordered)"+"\" visibility=1 itemRgb=\"On\"");
@@ -559,19 +564,23 @@ public class BrowserOutput
if (bgzip)
{
GZIPOutputStream pwzip = new GZIPOutputStream(new FileOutputStream(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed.gz"));
- String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+ byte[] btformat;
+ if (!bnobrowserheader)
+ {
+ String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\""+"\n";
- byte[] btformat = szout.getBytes();
- pwzip.write(btformat,0,btformat.length);
+ btformat = szout.getBytes();
+ pwzip.write(btformat,0,btformat.length);
- //pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
- // +" ordered)"+"\" visibility=2 itemRgb=\"On\"");
- int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
+ //pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+ // +" ordered)"+"\" visibility=2 itemRgb=\"On\"");
+ int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
- szout = "browser position "+szChroms[0]+":1-"+nbrowserend+"\n";
- btformat = szout.getBytes();
- pwzip.write(btformat,0,btformat.length);
- //pwzip.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ szout = "browser position "+szChroms[0]+":1-"+nbrowserend+"\n";
+ btformat = szout.getBytes();
+ pwzip.write(btformat,0,btformat.length);
+ //pwzip.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ }
for (int nlabel = szLabels.length-1; nlabel >=0; nlabel--)
{
@@ -641,10 +650,14 @@ public class BrowserOutput
else
{
PrintWriter pw = new PrintWriter(new FileWriter(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed"));
- pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+
+ if (!bnobrowserheader)
+ {
+ pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\"");
- int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
- pw.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
+ pw.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ }
for (int nlabel = szLabels.length-1; nlabel >=0; nlabel--)
{
@@ -802,20 +815,25 @@ public class BrowserOutput
if (bgzip)
{
+ byte[] btformat;
+
GZIPOutputStream pwzip = new GZIPOutputStream(new FileOutputStream(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed.gz"));
- String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
- +" ordered)"+"\" visibility=2 itemRgb=\"On\""+"\n";
- byte[] btformat = szout.getBytes();
- pwzip.write(btformat,0,btformat.length);
+ if (!bnobrowserheader)
+ {
+ String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+ +" ordered)"+"\" visibility=2 itemRgb=\"On\""+"\n";
+ btformat = szout.getBytes();
+ pwzip.write(btformat,0,btformat.length);
- //pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
- // +" ordered)"+"\" visibility=2 itemRgb=\"On\"");
- int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
+ //pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+ // +" ordered)"+"\" visibility=2 itemRgb=\"On\"");
+ int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
- szout = "browser position "+szChroms[0]+":1-"+nbrowserend+"\n";
- btformat = szout.getBytes();
- pwzip.write(btformat,0,btformat.length);
- //pwzip.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ szout = "browser position "+szChroms[0]+":1-"+nbrowserend+"\n";
+ btformat = szout.getBytes();
+ pwzip.write(btformat,0,btformat.length);
+ //pwzip.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ }
for (int nchrom = 0; nchrom < szChroms.length; nchrom++)
{
@@ -915,10 +933,14 @@ public class BrowserOutput
else
{
PrintWriter pw = new PrintWriter(new FileWriter(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed"));
- pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+ if (!bnobrowserheader)
+ {
+
+ pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\"");
- int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
- pw.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
+ pw.println("browser position "+szChroms[0]+":1-"+nbrowserend);
+ }
for (int nchrom = 0; nchrom < szChroms.length; nchrom++)
{
=====================================
edu/mit/compbio/ChromHMM/ChromHMM.java
=====================================
@@ -518,6 +518,11 @@ public class ChromHMM
*/
boolean bpseudo = false;
+ /**
+ * true if should skip the last input from pseudo
+ */
+ boolean bnopseudolast = false;
+
/**
* true if output should be zipped files
@@ -730,7 +735,7 @@ public class ChromHMM
boolean bprintsegment,boolean bprintstatebyline, int nbinsize,String szoutfileID,int nstateorder,boolean bordercols,int nzerotransitionpower,
Color theColor, boolean bnormalEM, int nmaxprocessors, boolean blowmem,
int numincludeseq, boolean bprintimage, boolean bscaleemissions,
- boolean bpseudo, boolean bgzip,boolean bsplit, boolean borderrows, boolean bscalebeta) throws IOException
+ boolean bpseudo, boolean bnopseudolast, boolean bgzip,boolean bsplit, boolean borderrows, boolean bscalebeta) throws IOException
{
this.szinputdir = szinputdir;
this.szoutputdir = szoutputdir;
@@ -764,6 +769,7 @@ public class ChromHMM
this.bprintimage = bprintimage;
this.bscaleemissions = bscaleemissions;
this.bpseudo = bpseudo;
+ this.bnopseudolast = bnopseudolast;
this.bgzip = bgzip;
this.bscalebeta = bscalebeta;
//this.numsplitbins = numsplitbins;
@@ -2066,10 +2072,12 @@ public class ChromHMM
int numels = alobservedpairflags.size();
//computes a tally for each flag combination observed of how frequently observed
- int[] tallys = new int[numels];
+ //int[] tallys = new int[numels];
+ long[] tallys = new long[numels];
//stores the total number of flag combinations observed
- int ntotaltally = 0;
+ //int ntotaltally = 0;
+ long ntotaltally = 0;
for (int nseq = 0; nseq < traindataObservedIndexPair.length; nseq++)
{
@@ -2095,7 +2103,8 @@ public class ChromHMM
//stores how many elements are currently assigned to the split node
- int[] partitionTally = new int[numstates];
+ //int[] partitionTally = new int[numstates];
+ long[] partitionTally = new long[numstates];
//initally everything gets assigned to split node 0
partitionTally[0] = ntotaltally;
@@ -2109,7 +2118,8 @@ public class ChromHMM
//stores for all prior splits how many elements would be split off
//if partitioning on that mark
- int[][] nextpartitionTally = new int[numstates-1][numdatasets];
+ //int[][] nextpartitionTally = new int[numstates-1][numdatasets];
+ long[][] nextpartitionTally = new long[numstates-1][numdatasets];
for (int niteration = 1; niteration < numstates; niteration++)
{
@@ -2119,7 +2129,8 @@ public class ChromHMM
{
//initializes the nextpartitionTally to 0
- int[] nextpartitionTally_ni = nextpartitionTally[ni];
+ //int[] nextpartitionTally_ni = nextpartitionTally[ni];
+ long[] nextpartitionTally_ni = nextpartitionTally[ni];
for (int nmark = 0; nmark < numdatasets; nmark++)
{
nextpartitionTally_ni[nmark] = 0;
@@ -2157,7 +2168,8 @@ public class ChromHMM
//considering all previous splits to split again
//fraction of total weighted elements in this node about to be split
- int partitionTally_nsplit = partitionTally[nsplit];
+ //int partitionTally_nsplit = partitionTally[nsplit];
+ long partitionTally_nsplit = partitionTally[nsplit];
double dprobfull = partitionTally_nsplit/(double) ntotaltally;
double dprobfullterm;
if (dprobfull> 0)
@@ -2170,7 +2182,8 @@ public class ChromHMM
dprobfullterm = 0;
}
- int[] nextpartitionTally_nsplit = nextpartitionTally[nsplit];
+ //int[] nextpartitionTally_nsplit = nextpartitionTally[nsplit];
+ long[] nextpartitionTally_nsplit = nextpartitionTally[nsplit];
for (int nsplitmark = 0; nsplitmark < numdatasets; nsplitmark++)
{
@@ -2216,7 +2229,8 @@ public class ChromHMM
}
//the number of elements in the new split
- int numnewsplit =nextpartitionTally[nbestsplit][nbestsplitmark];
+ //int numnewsplit =nextpartitionTally[nbestsplit][nbestsplitmark];
+ long numnewsplit =nextpartitionTally[nbestsplit][nbestsplitmark];
partitionTally[niteration] = numnewsplit;
//removes from the node we splitting from those we just split;
@@ -2237,7 +2251,8 @@ public class ChromHMM
}
}
- int[][] postally = new int[numstates][numdatasets];
+ //int[][] postally = new int[numstates][numdatasets];
+ long[][] postally = new long[numstates][numdatasets];
for (int nel = 0; nel < tallys.length; nel++)
{
@@ -2260,13 +2275,15 @@ public class ChromHMM
}
}
- int[] partitionTallySum = new int[partitionTally.length];
+ //int[] partitionTallySum = new int[partitionTally.length];
+ long[] partitionTallySum = new long[partitionTally.length];
for (int nstate = 1; nstate < numstates; nstate++)
{
//figures out how many descendants there are of each split
int ncurrstate = nstate;
- int ntotsum = 0;
- int ncurrval = partitionTally[ncurrstate];
+ //int ntotsum = 0;
+ //int ncurrval = partitionTally[ncurrstate];
+ long ncurrval = partitionTally[ncurrstate];
do
{
//incrementing counts for the parents
@@ -2288,8 +2305,11 @@ public class ChromHMM
//initialize the inital probability based on the partition of the first vector
- int[] numstarts = new int[numstates];
- int nvalidseq = 0;
+ //int[] numstarts = new int[numstates];
+ long[] numstarts = new long[numstates];
+ //int nvalidseq = 0;
+ long nvalidseq = 0;
+
for (int nseq = 0; nseq < traindataObservedIndexPair.length; nseq++)
{
if ((bincludeseq[nseq])&&(traindataObservedIndexPair[nseq].length > 0))
@@ -2308,7 +2328,8 @@ public class ChromHMM
//determining initial settings for the transition probability
- int[][] transitiontally = new int[numstates][numstates];
+ //int[][] transitiontally = new int[numstates][numstates];
+ long[][] transitiontally = new long[numstates][numstates];
int nnextstate;
for (int nseq = 0; nseq < traindataObservedIndexPair.length; nseq++)
{
@@ -2331,7 +2352,8 @@ public class ChromHMM
{
double[] transitionprobs_ni = transitionprobs[ni];
double dnumfromi = 0;
- int[] transitiontally_ni = transitiontally[ni];
+ //int[] transitiontally_ni = transitiontally[ni];
+ long[] transitiontally_ni = transitiontally[ni];
for (int nj = 0; nj < numstates; nj++)
{
@@ -2357,38 +2379,37 @@ public class ChromHMM
public void informationInitializeNested()
{
- //inital probability vector
- probinit = new double[numstates];
+ //inital probability vector
+ probinit = new double[numstates];
- //creates the emission probability matrix
- emissionprobs = new double[numstates][numdatasets][numbuckets];
+ //creates the emission probability matrix
+ emissionprobs = new double[numstates][numdatasets][numbuckets];
- //set to true if a transition has been eliminated
- elim = new boolean[numstates][numstates];
+ //set to true if a transition has been eliminated
+ elim = new boolean[numstates][numstates];
- //initalize the transition matrix
- transitionprobs = new double[numstates][numstates];
+ //initalize the transition matrix
+ transitionprobs = new double[numstates][numstates];
- //initialize index of the next non-zero transition
- transitionprobsindex = new int[numstates][numstates];
+ //initialize index of the next non-zero transition
+ transitionprobsindex = new int[numstates][numstates];
- //initalize number of non-zero transitions
- transitionprobsnum = new int[numstates];
+ //initalize number of non-zero transitions
+ transitionprobsnum = new int[numstates];
- //initalize column-wise index of non-zero transitions
- transitionprobsindexCol = new int[numstates][numstates];
+ //initalize column-wise index of non-zero transitions
+ transitionprobsindexCol = new int[numstates][numstates];
- //number of non-zero column transitions
- transitionprobsnumCol = new int[numstates];
+ //number of non-zero column transitions
+ transitionprobsnumCol = new int[numstates];
- int[][] traindataObservedIndexPair = new int[traindataObservedIndex.length][];
+ int[][] traindataObservedIndexPair = new int[traindataObservedIndex.length][];
+ ArrayList alobservedpairflags = new ArrayList(); //is an index from the element combination to the associated flags
- ArrayList alobservedpairflags = new ArrayList(); //is an index from the element combination to the associated flags
+ HashMap hmObserved= new HashMap(); //is an index from the associated flags to the element index
- HashMap hmObserved= new HashMap(); //is an index from the associated flags to the element index
-
- int nobserved= 0; //index on the unique observation combination we are observing
+ int nobserved= 0; //index on the unique observation combination we are observing
int[] samples= null;
@@ -2500,10 +2521,12 @@ public class ChromHMM
int numels = alobservedpairflags.size();
//computes a tally for each flag combination observed of how frequently observed
- int[] tallys = new int[numels];
+ //int[] tallys = new int[numels];
+ long[] tallys = new long[numels];
//stores the total number of flag combinations observed
- int ntotaltally = 0;
+ //int ntotaltally = 0;
+ long ntotaltally = 0;
for (int nseq = 0; nseq < traindataObservedIndexPair.length; nseq++)
{
@@ -2529,7 +2552,8 @@ public class ChromHMM
//stores how many elements are currently assigned to the split node
- int[] partitionTally = new int[numstates];
+ //int[] partitionTally = new int[numstates];
+ long[] partitionTally = new long[numstates];
//initally everything gets assigned to split node 0
partitionTally[0] = ntotaltally;
@@ -2543,7 +2567,8 @@ public class ChromHMM
//stores for all prior splits how many elements would be split off
//if partitioning on that mark
- int[][] nextpartitionTally = new int[numstates-1][numdatasets];
+ //int[][] nextpartitionTally = new int[numstates-1][numdatasets];
+ long[][] nextpartitionTally = new long[numstates-1][numdatasets];
for (int niteration = 1; niteration < numstates; niteration++)
{
@@ -2553,7 +2578,8 @@ public class ChromHMM
{
//initializes the nextpartitionTally to 0
- int[] nextpartitionTally_ni = nextpartitionTally[ni];
+ //int[] nextpartitionTally_ni = nextpartitionTally[ni];
+ long[] nextpartitionTally_ni = nextpartitionTally[ni];
for (int nmark = 0; nmark < numdatasets; nmark++)
{
nextpartitionTally_ni[nmark] = 0;
@@ -2591,7 +2617,8 @@ public class ChromHMM
//considering all previous splits to split again
//fraction of total weighted elements in this node about to be split
- int partitionTally_nsplit = partitionTally[nsplit];
+ //int partitionTally_nsplit = partitionTally[nsplit];
+ long partitionTally_nsplit = partitionTally[nsplit];
double dprobfull = partitionTally_nsplit/(double) ntotaltally;
double dprobfullterm;
if (dprobfull> 0)
@@ -2604,7 +2631,8 @@ public class ChromHMM
dprobfullterm = 0;
}
- int[] nextpartitionTally_nsplit = nextpartitionTally[nsplit];
+ //int[] nextpartitionTally_nsplit = nextpartitionTally[nsplit];
+ long[] nextpartitionTally_nsplit = nextpartitionTally[nsplit];
for (int nsplitmark = 0; nsplitmark < numdatasets; nsplitmark++)
{
@@ -2650,7 +2678,8 @@ public class ChromHMM
}
//the number of elements in the new split
- int numnewsplit =nextpartitionTally[nbestsplit][nbestsplitmark];
+ //int numnewsplit =nextpartitionTally[nbestsplit][nbestsplitmark];
+ long numnewsplit = nextpartitionTally[nbestsplit][nbestsplitmark];
partitionTally[niteration] = numnewsplit;
//removes from the node we splitting from those we just split;
@@ -2671,7 +2700,8 @@ public class ChromHMM
}
}
- int[][] postally = new int[numstates][numdatasets];
+ //int[][] postally = new int[numstates][numdatasets];
+ long[][] postally = new long[numstates][numdatasets];
for (int nel = 0; nel < tallys.length; nel++)
{
@@ -2694,13 +2724,15 @@ public class ChromHMM
}
}
- int[] partitionTallySum = new int[partitionTally.length];
+ //int[] partitionTallySum = new int[partitionTally.length];
+ long[] partitionTallySum = new long[partitionTally.length];
for (int nstate = 1; nstate < numstates; nstate++)
{
//figures out how many descendants there are of each split
int ncurrstate = nstate;
- int ntotsum = 0;
- int ncurrval = partitionTally[ncurrstate];
+ //int ntotsum = 0;
+ //int ncurrval = partitionTally[ncurrstate];
+ long ncurrval = partitionTally[ncurrstate];
do
{
//incrementing counts for the parents
@@ -2722,8 +2754,10 @@ public class ChromHMM
//initialize the inital probability based on the partition of the first vector
- int[] numstarts = new int[numstates];
- int nvalidseq = 0;
+ //int[] numstarts = new int[numstates];
+ long[] numstarts = new long[numstates];
+ //int nvalidseq = 0;
+ long nvalidseq = 0;
for (int nseq = 0; nseq < traindataObservedIndexPair.length; nseq++)
{
if ((bincludeseq[nseq])&&(traindataObservedIndexPair[nseq].length > 0))
@@ -2742,13 +2776,14 @@ public class ChromHMM
//determining initial settings for the transition probability
- int[][] transitiontally = new int[numstates][numstates];
+ //int[][] transitiontally = new int[numstates][numstates];
+ long[][] transitiontally = new long[numstates][numstates];
int nnextstate;
for (int nseq = 0; nseq < traindataObservedIndexPair.length; nseq++)
{
- if ((bincludeseq[nseq])&&(traindataObservedIndexPair[nseq].length > 0)) //updated in v1.14
- {
- //going through each sequence
+ if ((bincludeseq[nseq])&&(traindataObservedIndexPair[nseq].length > 0)) //updated in v1.14
+ {
+ //going through each sequence
int[] traindataObservedIndexPair_nseq = traindataObservedIndexPair[nseq];
int nprevstate = initStateAssign[traindataObservedIndexPair_nseq[0]];
for (int nindex = 1; nindex < traindataObservedIndexPair_nseq.length; nindex++)
@@ -2758,14 +2793,15 @@ public class ChromHMM
transitiontally[nprevstate][nnextstate]++;
nprevstate = nnextstate;
}
- }
+ }
}
for (int ni = 0; ni < numstates; ni++)
{
double[] transitionprobs_ni = transitionprobs[ni];
double dnumfromi = 0;
- int[] transitiontally_ni = transitiontally[ni];
+ //int[] transitiontally_ni = transitiontally[ni];
+ long[] transitiontally_ni = transitiontally[ni];
for (int nj = 0; nj < numstates; nj++)
{
@@ -3440,6 +3476,21 @@ public class ChromHMM
if (bscalebeta)
{
+
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -3524,6 +3575,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -3584,74 +3649,94 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns] /= ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
for (int nt = nlastindex - 1; nt >= 0; nt--)
{
- gamma_nt = gamma[nt];
- int ntp1 = (nt+1);
+ gamma_nt = gamma[nt];
+ int ntp1 = (nt+1);
- double[] emissionproducts_ncombo_ntp1 = emissionproducts[traindataObservedIndex_nseq[ntp1]];
+ double[] emissionproducts_ncombo_ntp1 = emissionproducts[traindataObservedIndex_nseq[ntp1]];
- double dsumbeta = 0;
- double dscale_nt = scale[nt];
+ double dsumbeta = 0;
+ double dscale_nt = scale[nt];
- for (int ns = 0; ns < numstates; ns++)
- {
- tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_ncombo_ntp1[ns];
- }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_ncombo_ntp1[ns];
+ }
- //double dscaleinv = 1.0/scale[nt];
- //scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
- for (int ni = 0; ni < numstates; ni++)
- {
- double dtempsum = 0;
- int[] transitionprobsindex_ni = transitionprobsindex[ni];
- double[] transitionprobs_ni = transitionprobs[ni];
- int transitionprobsnum_ni = transitionprobsnum[ni];
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
- if (transitionprobsnum_ni < nsparsecutoff)
- {
- //if it is sparse enough then it is worth the extra array indirection here
- for (int nj = 0; nj < transitionprobsnum_ni; nj++)
- {
- //for each state summing over transition probability to state j, emission probablity in j at next step
- //and probability of observing the remaining sequence
- nmappedindexouter = transitionprobsindex_ni[nj];
- dtempsum += transitionprobs_ni[nmappedindexouter]*tempproductbetaemiss[nmappedindexouter];
- }
- }
- else
- {
- for (int nj = 0; nj < numstates; nj++)
- {
- //for each state summing over transition probability to state j, emission probablity in j at next step
- //and probability of observing the remaining sequence
- dtempsum += transitionprobs_ni[nj]*tempproductbetaemiss[nj];
- }
- }
+ //double dscaleinv = 1.0/scale[nt];
+ //scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
+ for (int ni = 0; ni < numstates; ni++)
+ {
+ double dtempsum = 0;
+ int[] transitionprobsindex_ni = transitionprobsindex[ni];
+ double[] transitionprobs_ni = transitionprobs[ni];
+ int transitionprobsnum_ni = transitionprobsnum[ni];
- if (bscalebeta)
- {
- beta_nt[ni] = dtempsum;
- dsumbeta += dtempsum;
- }
- else
- {
- double dratio = dtempsum/dscale_nt;
- if (dratio > Double.MAX_VALUE)
- {
- beta_nt[ni] = Double.MAX_VALUE;//dtempsum/dscale_nt;
- }
- else
- {
- beta_nt[ni] = dratio;
- }
- }
+ if (transitionprobsnum_ni < nsparsecutoff)
+ {
+ //if it is sparse enough then it is worth the extra array indirection here
+ for (int nj = 0; nj < transitionprobsnum_ni; nj++)
+ {
+ //for each state summing over transition probability to state j, emission probablity in j at next step
+ //and probability of observing the remaining sequence
+ nmappedindexouter = transitionprobsindex_ni[nj];
+ dtempsum += transitionprobs_ni[nmappedindexouter]*tempproductbetaemiss[nmappedindexouter];
+ }
+ }
+ else
+ {
+ for (int nj = 0; nj < numstates; nj++)
+ {
+ //for each state summing over transition probability to state j, emission probablity in j at next step
+ //and probability of observing the remaining sequence
+ dtempsum += transitionprobs_ni[nj]*tempproductbetaemiss[nj];
+ }
+ }
+
+ if (bscalebeta)
+ {
+ beta_nt[ni] = dtempsum;
+ dsumbeta += dtempsum;
+ }
+ else
+ {
+ double dratio = dtempsum/dscale_nt;
+ if (dratio > Double.MAX_VALUE)
+ {
+ beta_nt[ni] = Double.MAX_VALUE;//dtempsum/dscale_nt;
+ }
+ else
+ {
+ beta_nt[ni] = dratio;
+ }
+ }
//double dratio = dtempsum/dscale_nt;
//if (dratio > Double.MAX_VALUE)
@@ -3680,22 +3765,25 @@ public class ChromHMM
ddenom = 0;
alpha_nt = alpha[nt];
- //gamma_nt - P(x=S| o_0,...,o_t)
- //P(o_t+1,...,o_T|x_t=s,lambda) * P(o_0,...,o_t,xt=s|lambda)
+ //gamma_nt - P(x=S| o_0,...,o_t)
+ //P(o_t+1,...,o_T|x_t=s,lambda) * P(o_0,...,o_t,xt=s|lambda)
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- double dval = alpha_nt[ns]*beta_nt[ns];
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ double dval = alpha_nt[ns]*beta_nt[ns];
- ddenom += dval;
- gamma_nt[ns] = dval;
- }
+ ddenom += dval;
+ gamma_nt[ns] = dval;
+ }
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns]/=ddenom;
- }
- beta_ntp1 = beta_nt;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns]/=ddenom;
+ }
+ }
+ beta_ntp1 = beta_nt;
}
@@ -4347,6 +4435,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -4431,6 +4533,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -4491,9 +4607,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns] /= ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
@@ -4511,6 +4630,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_ncombo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
//double dscaleinv = 1.0/scale[nt];
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
for (int ni = 0; ni < numstates; ni++)
@@ -4596,9 +4732,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns]/=ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns]/=ddenom;
+ }
}
beta_ntp1 = beta_nt;
}
@@ -5386,6 +5525,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -5469,6 +5622,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -5529,9 +5696,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns] /= ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
@@ -5549,6 +5719,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_ncombo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
//double dscaleinv = 1.0/scale[nt];
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
for (int ni = 0; ni < numstates; ni++)
@@ -5634,9 +5821,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns]/=ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns]/=ddenom;
+ }
}
beta_ntp1 = beta_nt;
}
@@ -6413,6 +6603,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -6500,6 +6704,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -6560,9 +6778,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns] /= ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
@@ -6580,6 +6801,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_ncombo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
//double dscaleinv = 1.0/scale[nt];
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
for (int ni = 0; ni < numstates; ni++)
@@ -6665,9 +6903,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns]/=ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns]/=ddenom;
+ }
}
beta_ntp1 = beta_nt;
}
@@ -7296,6 +7537,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -7375,8 +7630,22 @@ public class ChromHMM
scale[nt] = dscale;
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
- if (bscalebeta)
- {
+ if (bscalebeta)
+ {
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -7452,6 +7721,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_ncombo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
//double dscaleinv = 1.0/scale[nt];
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
for (int ni = 0; ni < numstates; ni++)
@@ -8001,6 +8287,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -8091,6 +8391,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -8156,9 +8470,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
+ if (ddenom > 0)
{
- gamma_nt[ns] /=ddenom;
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /=ddenom;
+ }
}
double[] gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex[nlastindex]];
@@ -8181,6 +8498,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_combo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
//double dscaleinv = 1.0/scale[nt];
double dsumbeta = 0;
double dscale_nt = scale[nt];
@@ -8270,9 +8604,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns] /= ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex[nt]];
@@ -8317,32 +8654,35 @@ public class ChromHMM
double dtempval = transitionprobs_ni[nj]*dalpha_nt_ni*tempproductbetaemiss[nj];
dsum += dtempval;
sumforsxi_ni[nj] = dtempval;
- }
+ }
}
}
-
- //normalizing the numerator by the sum of the denominator and updating this iterations value for it
- for (int ni = 0; ni < numstates; ni++)
- {
- int[] transitionprobsindex_ni = transitionprobsindex[ni];
- double[] sumforsxi_ni = sumforsxi[ni];
- double[] sxi_nseq_ni = sxi_nseq[ni];
- int ntransitionprobsnum_ni = transitionprobsnum[ni];
- if (ntransitionprobsnum_ni < nsparsecutoff)
+ if (dsum > 0)
+ {
+ //normalizing the numerator by the sum of the denominator and updating this iterations value for it
+ for (int ni = 0; ni < numstates; ni++)
{
- //guessing sparse enough to avoid the indirections
- for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
- {
- int nmappedindex = transitionprobsindex_ni[nj];
- sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
+ int[] transitionprobsindex_ni = transitionprobsindex[ni];
+ double[] sumforsxi_ni = sumforsxi[ni];
+ double[] sxi_nseq_ni = sxi_nseq[ni];
+ int ntransitionprobsnum_ni = transitionprobsnum[ni];
+
+ if (ntransitionprobsnum_ni < nsparsecutoff)
+ {
+ //guessing sparse enough to avoid the indirections
+ for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
+ {
+ int nmappedindex = transitionprobsindex_ni[nj];
+ sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
+ }
}
- }
- else
- {
- for (int nj = 0; nj < numstates; nj++)
- {
- sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
+ else
+ {
+ for (int nj = 0; nj < numstates; nj++)
+ {
+ sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
+ }
}
}
}
@@ -8412,7 +8752,7 @@ public class ChromHMM
dgammainitsum += gammainitstore[nitr][ni];
}
- if (bpseudo)
+ if ((bpseudo)&&(!bnopseudolast))
{
dgammainitsum++;
}
@@ -8543,7 +8883,7 @@ public class ChromHMM
emissionprobs_ns_nmark[nbucket] += gammaksumstore[nitr][ns][nmark][nbucket];
}
- if (bpseudo)
+ if ((bpseudo) && ((!bnopseudolast)||(nmark<emissionprobs_ns.length-1)))
{
emissionprobs_ns_nmark[nbucket]++;
}
@@ -8910,6 +9250,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -8998,6 +9352,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -9057,9 +9425,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
+ if (ddenom > 0)
{
- gamma_nt[ns] /=ddenom;
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /=ddenom;
+ }
}
double[] gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex_nseq[nlastindex]];
@@ -9082,6 +9453,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_combo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
//double dscaleinv = 1.0/scale[nt];
double dsumbeta = 0;
double dscale_nt = scale[nt];
@@ -9166,10 +9554,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
-
- for (int ns = 0; ns < gamma_nt.length; ns++)
- {
- gamma_nt[ns] /= ddenom;
+ if (ddenom > 0)
+ {
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex_nseq[nt]];
@@ -9218,28 +9608,31 @@ public class ChromHMM
}
}
- //normalizing the numerator by the sum of the denominator and updating this iterations value for it
- for (int ni = 0; ni < numstates; ni++)
- {
- int[] transitionprobsindex_ni = transitionprobsindex[ni];
- double[] sumforsxi_ni = sumforsxi[ni];
- double[] sxi_nseq_ni = sxi_nseq[ni];
- int ntransitionprobsnum_ni = transitionprobsnum[ni];
-
- if (ntransitionprobsnum_ni < nsparsecutoff)
+ if (dsum > 0)
+ {
+ //normalizing the numerator by the sum of the denominator and updating this iterations value for it
+ for (int ni = 0; ni < numstates; ni++)
{
- //guessing sparse enough to avoid the indirections
- for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
- {
- int nmappedindex = transitionprobsindex_ni[nj];
- sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
+ int[] transitionprobsindex_ni = transitionprobsindex[ni];
+ double[] sumforsxi_ni = sumforsxi[ni];
+ double[] sxi_nseq_ni = sxi_nseq[ni];
+ int ntransitionprobsnum_ni = transitionprobsnum[ni];
+
+ if (ntransitionprobsnum_ni < nsparsecutoff)
+ {
+ //guessing sparse enough to avoid the indirections
+ for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
+ {
+ int nmappedindex = transitionprobsindex_ni[nj];
+ sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
+ }
}
- }
- else
- {
- for (int nj = 0; nj < numstates; nj++)
- {
- sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
+ else
+ {
+ for (int nj = 0; nj < numstates; nj++)
+ {
+ sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
+ }
}
}
}
@@ -9309,7 +9702,7 @@ public class ChromHMM
dgammainitsum += gammainitstore[nitr][ni];
}
- if (bpseudo)
+ if ((bpseudo)&&(!bnopseudolast))
{
dgammainitsum++;
}
@@ -9441,7 +9834,7 @@ public class ChromHMM
}
- if (bpseudo)
+ if ((bpseudo) && ((!bnopseudolast)||(nmark<emissionprobs_ns.length-1)))
{
emissionprobs_ns_nmark[nbucket]++;
}
@@ -9703,6 +10096,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -9784,6 +10191,20 @@ public class ChromHMM
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -9841,9 +10262,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
+ if (ddenom > 0)
{
- gamma_nt[ns] /=ddenom;
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /=ddenom;
+ }
}
double[] gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex_nseq[nlastindex]];
@@ -9866,6 +10290,23 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_combo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
double dsumbeta = 0;
//double dscaleinv = 1.0/scale[nt];
double dscale_nt = scale[nt];
@@ -9946,9 +10387,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
+ if (ddenom > 0)
{
- gamma_nt[ns] /= ddenom;
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex_nseq[nt]];
@@ -9997,30 +10441,33 @@ public class ChromHMM
}
}
- //normalizing the numerator by the sum of the denominator and updating this iterations value for it
- for (int ni = 0; ni < numstates; ni++)
+ if (dsum > 0)
{
- int[] transitionprobsindex_ni = transitionprobsindex[ni];
- double[] sumforsxi_ni = sumforsxi[ni];
- double[] sxi_nseq_ni = sxi_nseq[ni];
- int ntransitionprobsnum_ni = transitionprobsnum[ni];
+ //normalizing the numerator by the sum of the denominator and updating this iterations value for it
+ for (int ni = 0; ni < numstates; ni++)
+ {
+ int[] transitionprobsindex_ni = transitionprobsindex[ni];
+ double[] sumforsxi_ni = sumforsxi[ni];
+ double[] sxi_nseq_ni = sxi_nseq[ni];
+ int ntransitionprobsnum_ni = transitionprobsnum[ni];
- if (ntransitionprobsnum_ni < nsparsecutoff)
- {
- //guessing sparse enough to avoid the indirections
- for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
- {
- int nmappedindex = transitionprobsindex_ni[nj];
- sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
- }
- }
- else
- {
- for (int nj = 0; nj < numstates; nj++)
- {
- sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
- }
- }
+ if (ntransitionprobsnum_ni < nsparsecutoff)
+ {
+ //guessing sparse enough to avoid the indirections
+ for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
+ {
+ int nmappedindex = transitionprobsindex_ni[nj];
+ sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
+ }
+ }
+ else
+ {
+ for (int nj = 0; nj < numstates; nj++)
+ {
+ sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
+ }
+ }
+ }
}
beta_ntp1 = beta_nt; //updating beta_ntp1
}
@@ -10559,6 +11006,20 @@ public class ChromHMM
//converts the alpha terms to probabilities
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[0] = dscale;
+ }
+
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
@@ -10632,21 +11093,39 @@ public class ChromHMM
dscale += dalphaval;
}
+
//rescaling alpha
scale[nt] = dscale;
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
if (bscalebeta)
{
+ if (dscale == 0)
+ {
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ //added
+ if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
+ {
+ alpha_nt[ns] = EPSILONSTATE;
+ dscale += EPSILONSTATE;
+ }
+ }
+ scale[nt] = dscale;
+ }
+
+ // else
+ //{
for (int ns = 0; ns < numstates; ns++)
{
alpha_nt[ns] /= dscale;
if ((alpha_nt[ns] < EPSILONSTATE)&&(emissionproducts_nobserveindex[ns]>0))//(ns < numstates-1)))
{
- alpha_nt[ns] = EPSILONSTATE;
+ alpha_nt[ns] = EPSILONSTATE;
}
- }
+ }
+ //}
}
else
{
@@ -10703,9 +11182,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
+ if (ddenom > 0)
{
- gamma_nt[ns] /=ddenom;
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /=ddenom;
+ }
}
double[] gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex[nlastindex]];
@@ -10728,7 +11210,25 @@ public class ChromHMM
tempproductbetaemiss[ns] = beta_ntp1[ns]*emissionproducts_combo_ntp1[ns];
}
+ if (bscaleemissions)
+ {
+ //adding here to help numerical stability
+ double dmaxval = 0;
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ if (tempproductbetaemiss[ns] > dmaxval)
+ {
+ dmaxval = tempproductbetaemiss[ns];
+ }
+ }
+ for (int ns = 0; ns < numstates; ns++)
+ {
+ tempproductbetaemiss[ns] = tempproductbetaemiss[ns]/dmaxval;
+ }
+ }
+
double dsumbeta = 0;
+
//double dscaleinv = 1.0/scale[nt];
double dscale_nt = scale[nt];
//scale_t(s)=P(o_0,...,o_t|lambda) summed over all states
@@ -10817,9 +11317,12 @@ public class ChromHMM
gamma_nt[ns] = dval;
}
- for (int ns = 0; ns < gamma_nt.length; ns++)
+ if (ddenom > 0)
{
- gamma_nt[ns] /= ddenom;
+ for (int ns = 0; ns < gamma_nt.length; ns++)
+ {
+ gamma_nt[ns] /= ddenom;
+ }
}
gammaObservedSum_combo_nt = gammaObservedSum[traindataObservedIndex[nt]];
@@ -10853,6 +11356,7 @@ public class ChromHMM
//computes transition probability from state i to j
double dtempval = transitionprobs_ni[nmappedindex] *dalpha_nt_ni*tempproductbetaemiss[nmappedindex];
dsum += dtempval;
+
sumforsxi_ni[nmappedindex] = dtempval;
}
}
@@ -10866,33 +11370,38 @@ public class ChromHMM
sumforsxi_ni[nj] = dtempval;
}
}
- }
-
- //normalizing the numerator by the sum of the denominator and updating this iterations value for it
- for (int ni = 0; ni < numstates; ni++)
+ }
+
+
+ if (dsum > 0)
{
- int[] transitionprobsindex_ni = transitionprobsindex[ni];
- double[] sumforsxi_ni = sumforsxi[ni];
- double[] sxi_nseq_ni = sxi_nseq[ni];
- int ntransitionprobsnum_ni = transitionprobsnum[ni];
+ //added to avoid numerical errors
+ //normalizing the numerator by the sum of the denominator and updating this iterations value for it
+ for (int ni = 0; ni < numstates; ni++)
+ {
+ int[] transitionprobsindex_ni = transitionprobsindex[ni];
+ double[] sumforsxi_ni = sumforsxi[ni];
+ double[] sxi_nseq_ni = sxi_nseq[ni];
+ int ntransitionprobsnum_ni = transitionprobsnum[ni];
- if (ntransitionprobsnum_ni < nsparsecutoff)
- {
- //guessing sparse enough to avoid the indirections
- for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
- {
- int nmappedindex = transitionprobsindex_ni[nj];
- sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
- }
- }
- else
- {
- for (int nj = 0; nj < numstates; nj++)
- {
- sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
- }
- }
- }
+ if (ntransitionprobsnum_ni < nsparsecutoff)
+ {
+ //guessing sparse enough to avoid the indirections
+ for (int nj = 0; nj < ntransitionprobsnum_ni; nj++)
+ {
+ int nmappedindex = transitionprobsindex_ni[nj];
+ sxi_nseq_ni[nmappedindex] += sumforsxi_ni[nmappedindex]/dsum;
+ }
+ }
+ else
+ {
+ for (int nj = 0; nj < numstates; nj++)
+ {
+ sxi_nseq_ni[nj] += sumforsxi_ni[nj]/dsum;
+ }
+ }
+ }
+ }
beta_ntp1 = beta_nt; //updating beta_ntp1
}
@@ -11322,9 +11831,9 @@ public class ChromHMM
dgammainitsum += gammainitstore[nitr][ni];
}
- if (bpseudo)
+ if ((bpseudo)&&(!bnopseudolast))
{
- dgammainitsum++;
+ dgammainitsum++;
}
probinit[ni] = dgammainitsum;
dsum += dgammainitsum;
@@ -11372,6 +11881,7 @@ public class ChromHMM
{
int ntransitionprobsindex_ni_nj = transitionprobsindex_ni[nj];
//computes the updated transition probabilities
+
transitionprobs_ni[ntransitionprobsindex_ni_nj] /= dsum;
if ((transitionprobs_ni[ntransitionprobsindex_ni_nj] < dzerotransitioncutoff) && (ni != ntransitionprobsindex_ni_nj))
@@ -11453,6 +11963,7 @@ public class ChromHMM
emissionprobs_ns_nmark[nbucket] = 0;
//ncurrnumincludeseq
//for (int nitr = 0; nitr < chromfiles.length; nitr++) //was traindataobserved length
+ //double dtempsum = 0;
for (int nitr = 0; nitr < ncurrnumincludeseq; nitr++) //was traindataobserved length
{
//if (bincludeseq[nitr])
@@ -11461,7 +11972,7 @@ public class ChromHMM
//}
}
- if (bpseudo)
+ if ((bpseudo) && ((!bnopseudolast)||(nmark<emissionprobs_ns.length-1)))
{
emissionprobs_ns_nmark[nbucket]++;
}
@@ -11939,7 +12450,7 @@ public class ChromHMM
}
}
- if (bpseudo)
+ if ((bpseudo)&&(!bnopseudolast))
{
dgammainitsum++;
}
@@ -12077,7 +12588,7 @@ public class ChromHMM
}
}
- if (bpseudo)
+ if ((bpseudo) && ((!bnopseudolast)||(nmark<emissionprobs_ns.length-1)))
{
emissionprobs_ns_nmark[nbucket]++;
}
@@ -12848,7 +13359,7 @@ public class ChromHMM
if (szcommand.equalsIgnoreCase("Version"))
{
- System.out.println("This is Version 1.24 of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology");
+ System.out.println("This is Version 1.25 of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology");
}
else if ((szcommand.equals("BinarizeBam"))||(szcommand.equalsIgnoreCase("BinarizeBed")))
{
@@ -13933,6 +14444,7 @@ public class ChromHMM
String szlabelmapping = null;
boolean bgzip = false;
boolean blowmem = false;
+ boolean bnobrowserheader = false;
int nargindex = 1;
int numstates = -1;
@@ -13946,6 +14458,10 @@ public class ChromHMM
{
bgzip = true;
}
+ else if (args[nargindex].equals("-nobrowserheader"))
+ {
+ bnobrowserheader = true;
+ }
else if ((args[nargindex].equals("-l"))||(args[nargindex].equals("-m")))
{
//the -l is for backwards compatibility
@@ -13973,7 +14489,7 @@ public class ChromHMM
String szsegmentationname = args[nargindex++];
String szoutputfileprefix =args[nargindex];
BrowserOutput theBrowserOutput = new BrowserOutput(szsegmentfile,szcolormapping,szlabelmapping,
- szsegmentationname, szoutputfileprefix,numstates,bgzip);
+ szsegmentationname, szoutputfileprefix,numstates,bgzip, bnobrowserheader);
theBrowserOutput.makebrowserdense();
if (blowmem)
{
@@ -13991,7 +14507,7 @@ public class ChromHMM
if (!bok)
{
- System.out.println("usage: MakeBrowserFiles [-c colormappingfile][-gzip][-lowmem][-m labelmappingfile][-n numstates] segmentfile segmentationname outputfileprefix");
+ System.out.println("usage: MakeBrowserFiles [-c colormappingfile][-gzip][-lowmem][-m labelmappingfile][-n numstates][-nobrowserheader] segmentfile segmentationname outputfileprefix");
}
}
else if (szcommand.equalsIgnoreCase("OverlapEnrichment"))
@@ -14382,10 +14898,12 @@ public class ChromHMM
boolean bnoprintsegment = false;
boolean bprintbrowser = true;
boolean bprintenrich = true;
+ boolean bnobrowserheader = false;
boolean bprintimage = true;
boolean blowmem = false;
boolean bscaleemissions = false;
boolean bpseudo = false;
+ boolean bnopseudolast = false;
boolean bgzip = false;
boolean bsplit = false;
int numsplitbins = ChromHMM.DEFAULT_NUMSPLITBINS;
@@ -14510,6 +15028,10 @@ public class ChromHMM
{
bprintbrowser = false;
}
+ else if (args[nargindex].equals("-nobrowserheader"))
+ {
+ bnobrowserheader = true;
+ }
else if (args[nargindex].equals("-noenrich"))
{
bprintenrich = false;
@@ -14527,6 +15049,10 @@ public class ChromHMM
{
bpseudo = true;
}
+ else if (args[nargindex].equals("-nopseudolast"))
+ {
+ bnopseudolast = true;
+ }
else if (args[nargindex].equals("-stateordering"))
{
String sztoken = args[++nargindex];
@@ -14693,7 +15219,7 @@ public class ChromHMM
szInitFile,dloadsmoothemission,dloadsmoothtransition,dinformationsmooth,
nmaxiterations,dconvergediff,nmaxseconds, bprintposterior,bprintsegments,bprintstatebyline,
nbinsize,szoutfileID,nstateorder,bordercols,nzerotransitionpower,theColor,bnormalEM, nmaxprocessors,
- blowmem,numincludeseq,bprintimage,bscaleemissions, bpseudo, bgzip, bsplit, borderrows, bscalebeta);
+ blowmem,numincludeseq,bprintimage,bscaleemissions, bpseudo,bnopseudolast, bgzip, bsplit, borderrows, bscalebeta);
theHMM.buildModel();
@@ -14810,7 +15336,7 @@ public class ChromHMM
BrowserOutput theBrowserOutput = new BrowserOutput(szsegmentfile,null,null,
- szprefix,szoutputdir+"/"+szprefix,numstates,bgzip);
+ szprefix,szoutputdir+"/"+szprefix,numstates,bgzip,bnobrowserheader);
theBrowserOutput.makebrowserdense();
if (blowmem)
@@ -14979,7 +15505,7 @@ public class ChromHMM
{
System.out.println("usage: LearnModel [-b binsize][-color r,g,b][-d convergedelta][-e loadsmoothemission][-f inputfilelist][-gzip][-h informationsmooth]"+
"[-holdcolumnorder][-holdroworder][-i outfileID][-init information|random|load][-l chromosomelengthfile][-lowmem][-m modelinitialfile][-many]"+
- "[-n numseq][-noautoopen][-nobed][-nobrowser][-noenrich][-noimage][-p maxprocessors][-pseudo][-printposterior][-printstatebyline][-r maxiterations][-s seed][-scalebeta]"+
+ "[-n numseq][-noautoopen][-nobed][-nobrowser][-nobrowserheader][-noenrich][-noimage][-nopseudolast][-p maxprocessors][-pseudo][-printposterior][-printstatebyline][-r maxiterations][-s seed][-scalebeta]"+
"[-splitrows][-stateordering emission|transition]"+
"[-t loadsmoothtransition][-u coorddir][-v anchorfiledir][-x maxseconds][-z zerotransitionpower] inputdir outputdir numstates assembly");
}
=====================================
edu/mit/compbio/ChromHMM/ConvertGeneTable.java
=====================================
@@ -208,13 +208,14 @@ public class ConvertGeneTable
}
else
{
- String szbin = null;
if (!bnobin)
{
+ //updated in 1.25
+ String szbin = null;
szbin = st.nextToken().trim();
+ if (!szbin.equals("\t"))
+ st.nextToken().trim();
}
- if (!szbin.equals("\t"))
- st.nextToken().trim();
String szname = st.nextToken().trim();
if (!szname.equals("\t"))
st.nextToken().trim();
=====================================
versionlog.txt
=====================================
@@ -1,3 +1,16 @@
+12/28/2023 ChromHMM 1.25
+* Added the flag '-nobrowserheader' to LearnModel and MakeBrowserFiles to surpress the printing of header lines in browser bed files
+* Added the flag '-nopseudoinit' to LearnModel which prevents pseudocounts from being added in computing the emission parameter of the last mark and
+also in the initial state probabilities. This allows dummy variables/states to still be used with pseudo counts.
+* Fixed a bug when applying ConvertGeneTable with the '-nobin' flag
+* Handled a numerical overflow issue with the LearnModel when the number of bins exceeded the maximum Java integer value by changing to the use of long
+* Added increased numerical stability with additional checks if certain values are 0, which would be because of numerical stability issues, before dividing
+by them
+* Added further increased numerical stability when using the '-many' flag
+* Added further increased numerical stability when using the '-scalebeta' flag
+* Now compiled to target a minimum of Java 1.7 from 1.6
+
+
12/29/2022 ChromHMM 1.24
* Added '-browser' flag to OverlapEnrichment and NeighborhoodEnrichment to allow computing enrichments with browser bed files, which ignores lines
that begin with 'browser' or 'track'
View it on GitLab: https://salsa.debian.org/med-team/chromhmm/-/compare/db10de5fcb2d14954bc4ee67259c3b775da094b7...b6f2ef790556980469aa8cd534be8cc332c91937
--
View it on GitLab: https://salsa.debian.org/med-team/chromhmm/-/compare/db10de5fcb2d14954bc4ee67259c3b775da094b7...b6f2ef790556980469aa8cd534be8cc332c91937
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