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ChromHMM Version 1.22
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@jernst98
jernst98 committed Oct 24, 2020
1 parent ed404f0 commit 515c2bf
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Showing 6 changed files with 378 additions and 99 deletions.
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261 changes: 239 additions & 22 deletions edu/mit/compbio/ChromHMM/ChromHMM.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2911,7 +2911,7 @@ public void loadModelSmooth(double dproceduresmoothemission, double dproceduresm
}
chorder = st.nextToken().charAt(0);

if ((nstateorder != ChromHMM.STATEORDER_TRANSITION)&&(nstateorder != ChromHMM.STATEORDER_EMISSION))
if ((nstateorder != ChromHMM.STATEORDER_TRANSITION)&&(nstateorder != ChromHMM.STATEORDER_EMISSION)&&(nstateorder != ChromHMM.STATEORDER_FIXED))
{
nstateorder = -1;
for (int ni = 0; ni < ChromHMM.ORDERCHARS.length; ni++)
Expand Down Expand Up @@ -7029,7 +7029,7 @@ public int getMaxStateAtPos(int[][] data, int npos) throws IOException
double[][] alpha = new double[data.length][numstates];

//Temporary storage of the gamma's for each state
double[][] gamma = new double[data.length][numstates];
//double[][] gamma = new double[data.length][numstates];

//Temporary storage of the beta values for each state
double[] beta_nt = new double[numstates];
Expand Down Expand Up @@ -12848,10 +12848,11 @@ public static void main(String[] args) throws IOException

if (szcommand.equalsIgnoreCase("Version"))
{
System.out.println("This is Version 1.21 of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology");
System.out.println("This is Version 1.22 of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology");
}
else if ((szcommand.equals("BinarizeBam"))||(szcommand.equalsIgnoreCase("BinarizeBed")))
{
boolean bstacked = false;
boolean bgzip = false;
boolean bpairend = false;
boolean bsplit = false;
Expand All @@ -12877,6 +12878,12 @@ else if ((szcommand.equals("BinarizeBam"))||(szcommand.equalsIgnoreCase("Binariz
boolean bshift = false;
boolean bflagsplitbins = false;

boolean bflagsplitcols = false;

boolean bsplitcols = false;
int nnummarksplit = 10;
int nmarksplitindex = -1;

int nargindex = 1;
if (args.length <= 4)
{
Expand Down Expand Up @@ -12926,6 +12933,16 @@ else if (args[nargindex].equals("-j"))
bflagsplitbins = true;
//bsplit = true;
}
else if (args[nargindex].equals("-k"))
{
nmarksplitindex = Integer.parseInt(args[++nargindex]);
bflagsplitcols = true;
}
else if (args[nargindex].equals("-m"))
{
nnummarksplit = Integer.parseInt(args[++nargindex]);
bflagsplitcols = true;
}
else if (args[nargindex].equals("-n"))
{
nshift = Integer.parseInt(args[++nargindex]);
Expand Down Expand Up @@ -12955,6 +12972,14 @@ else if (args[nargindex].equals("-splitrows"))
{
bsplit = true;
}
else if (args[nargindex].equals("-splitcols"))
{
bsplitcols = true;
}
else if (args[nargindex].equals("-stacked"))
{
bstacked = true;
}
else if (args[nargindex].equals("-strictthresh"))
{
bcontainsthresh = false;
Expand Down Expand Up @@ -13015,6 +13040,12 @@ else if (args[nargindex].equals("-w"))
bok = false;
}

if ((!bsplitcols)&&(bflagsplitcols))
{
bok = false;
}



if ((bok)&&(nargindex == args.length-4))
{
Expand All @@ -13037,26 +13068,208 @@ else if (args[nargindex].equals("-w"))
szcontroldir = szmarkdir;
}



int nmaxsplit = 0;
if (bsplitcols)
{
String szLineCellMark;
int ncellmarkline = 0;

BufferedReader brcellmark = Util.getBufferedReader(szcellmarkfiletable);
HashSet hscombo = new HashSet();

while ((szLineCellMark=brcellmark.readLine()) != null)
{
if (szLineCellMark.trim().equals("")) continue;

StringTokenizer stcellmark = new StringTokenizer(szLineCellMark,"\t");

if (stcellmark.countTokens() < 3)
{
throw new IllegalArgumentException("In "+szcellmarkfiletable+" "+szLineCellMark+" does not have at least three columns");
}
String szcell = stcellmark.nextToken().trim(); //added trim in v1.20 to remove leading and trailing white space
String szmark = stcellmark.nextToken().trim();

if (hscombo.contains(szcell+"\t"+szmark))
{
throw new IllegalArgumentException("In "+szcellmarkfiletable+" "+szcell+"\t"+szmark+" found twice, but -splitcols specified");
}
hscombo.add(szcell+"\t"+szmark);

if (ncellmarkline % nnummarksplit == 0)
{
nmaxsplit++;
}
ncellmarkline++;
}
brcellmark.close();
}

if (nsplitindex >= 0)
{
if (bpeaks)
{
Preprocessing.makeBinaryDataFromPeaksSplit(szchromlengthfile, szmarkdir, szoutputbinarydir, szcellmarkfiletable,
nbinsize, bgzip, numsplitbins, nsplitindex, noffsetleft,noffsetright);
}
else
{
bok = false;
}
if (bpeaks)
{
if ((bsplitcols)&&(nmarksplitindex==-1))
{
//need to figure out maxsplit

for (nmarksplitindex = 0; nmarksplitindex < nmaxsplit; nmarksplitindex++)
{
String szoutputbinarydirsub = szoutputbinarydir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputbinarydirsub);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputbinarydirsub+" does not exist and could not be created!");
}
}

Preprocessing.makeBinaryDataFromPeaksSplit(szchromlengthfile, szmarkdir, szoutputbinarydir, szcellmarkfiletable,
nbinsize, bgzip, numsplitbins, nsplitindex, noffsetleft,noffsetright,
bsplitcols,nnummarksplit,nmarksplitindex,bstacked);
}
}
else
{
if (bsplitcols)
{
if (nmarksplitindex >= nmaxsplit)
{
throw new IllegalArgumentException("nmarksplitindex"+" value of "+nmarksplitindex+" is greater than the maximum of "+(nmaxsplit-1));
}
szoutputbinarydir = szoutputbinarydir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputbinarydir);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputbinarydir+" does not exist and could not be created!");
}
}
}

Preprocessing.makeBinaryDataFromPeaksSplit(szchromlengthfile, szmarkdir, szoutputbinarydir, szcellmarkfiletable,
nbinsize, bgzip, numsplitbins, nsplitindex, noffsetleft,noffsetright,
bsplitcols,nnummarksplit,nmarksplitindex, bstacked);
}
}
else
{
bok = false;
}
}
else
{
Preprocessing.makeBinaryDataFromBed(szchromlengthfile,szmarkdir,szcontroldir,nflankwidthcontrol,szcellmarkfiletable,

if ((bsplitcols)&&(nmarksplitindex==-1))
{
//going through all
//need to figure out maxsplit

for (nmarksplitindex = 0; nmarksplitindex < nmaxsplit; nmarksplitindex++)
{
String szoutputbinarydirsub = szoutputbinarydir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputbinarydirsub);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputbinarydirsub+" does not exist and could not be created!");
}
}

String szoutputsignaldirsub = null;
if (szoutputsignaldir != null)
{
szoutputsignaldirsub = szoutputsignaldir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputsignaldirsub);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputsignaldirsub+" does not exist and could not be created!");
}
}
}

String szoutputcontroldirsub = null;
if (szoutputcontroldirsub != null)
{
szoutputcontroldirsub = szoutputcontroldir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputcontroldirsub);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputcontroldirsub+" does not exist and could not be created!");
}
}
}

Preprocessing.makeBinaryDataFromBed(szchromlengthfile,szmarkdir,szcontroldir,nflankwidthcontrol,szcellmarkfiletable,
nshift,bcenterinterval, noffsetleft,noffsetright,szoutputsignaldir,
szoutputbinarydirsub,szoutputcontroldir,
dpoissonthresh,dfoldthresh,bcontainsthresh,
npseudocountcontrol,nbinsize,szcolfields,bpeaks, dcountthresh,szcommand.equalsIgnoreCase("BinarizeBam"),
bpairend, bgzip, bsplit, numsplitbins, bsplitcols,nnummarksplit,nmarksplitindex, bstacked);
}
}
else
{
if (bsplitcols)
{
if (nmarksplitindex >= nmaxsplit)
{
throw new IllegalArgumentException("nmarksplitindex"+" value of "+nmarksplitindex+" is greater than the maximum of "+(nmaxsplit-1));
}
szoutputbinarydir = szoutputbinarydir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputbinarydir);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputbinarydir+" does not exist and could not be created!");
}
}

if (szoutputsignaldir != null)
{
szoutputsignaldir = szoutputsignaldir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputsignaldir);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputsignaldir+" does not exist and could not be created!");
}
}
}

if (szoutputcontroldir != null)
{
szoutputcontroldir = szoutputcontroldir+"/SET"+(nmarksplitindex+1);
f = new File(szoutputcontroldir);
if (!f.exists())
{
if (!f.mkdirs())
{
throw new IllegalArgumentException(szoutputcontroldir+" does not exist and could not be created!");
}
}
}
}

Preprocessing.makeBinaryDataFromBed(szchromlengthfile,szmarkdir,szcontroldir,nflankwidthcontrol,szcellmarkfiletable,
nshift,bcenterinterval, noffsetleft,noffsetright,szoutputsignaldir,
szoutputbinarydir,szoutputcontroldir,
dpoissonthresh,dfoldthresh,bcontainsthresh,
npseudocountcontrol,nbinsize,szcolfields,bpeaks, dcountthresh,szcommand.equalsIgnoreCase("BinarizeBam"),
bpairend, bgzip, bsplit, numsplitbins);
bpairend, bgzip, bsplit, numsplitbins, bsplitcols,nnummarksplit,nmarksplitindex,bstacked);

}
}
}
else
Expand All @@ -13071,15 +13284,15 @@ else if (args[nargindex].equals("-w"))
{
//v1.18 update
System.out.println("usage BinarizeBed [-b binsize][-c controldir][-center][-colfields chromosome,start,end[,strand]][-e offsetend][-f foldthresh]"+
"[-g signalthresh][-gzip][-n shift][-o outputcontroldir][-p poissonthresh][-peaks [-i splitindex]][-s offsetstart][-splitrows [-j numsplitbins]][-strictthresh][-t outputsignaldir]"+
"[-g signalthresh][-gzip][-n shift][-o outputcontroldir][-p poissonthresh][-peaks [-i splitrowindex]][-s offsetstart][-splitcols [-k splitcolindex][-m numsplitcols]][-splitrows [-j numsplitbins]][-stacked][-strictthresh][-t outputsignaldir]"+
"[-u pseudocountcontrol][-w flankwidthcontrol] "+
"chromosomelengthfile inputbeddir cellmarkfiletable outputbinarydir");
}
else
{
System.out.println("usage BinarizeBam [-b binsize][-c controldir][-e offsetend][-f foldthresh]"+
"[-g signalthresh][-gzip][-o outputcontroldir][-p poissonthresh][-paired|[-center][-n shift][-peaks [-i splitindex]]"+
"[-s offsetstart][-splitrows [-j numsplitbins]][-strictthresh][-t outputsignaldir]"+
"[-g signalthresh][-gzip][[-o outputcontroldir][-p poissonthresh][-paired|[-center][-n shift][-peaks [-i splitindex]]"+
"[-s offsetstart][-splitcols [-k splitcolindex][-m numsplitcols]][-splitrows [-j numsplitbins]][-stacked][-strictthresh][-t outputsignaldir]"+
"[-u pseudocountcontrol][-w flankwidthcontrol] "+
"chromosomelengthfile inputbamdir cellmarkfiletable outputbinarydir");
}
Expand Down Expand Up @@ -13217,7 +13430,7 @@ else if (szcommand.equalsIgnoreCase("MergeBinary"))
int numsplitbins = ChromHMM.DEFAULT_NUMSPLITBINS;
boolean bsplit = false;
String szdirlistfile = null;

String sztype = "binary";
String szinputdir = null;
String szoutputdir = null;
boolean bflagsplitbins = false;
Expand All @@ -13237,6 +13450,10 @@ else if (szcommand.equalsIgnoreCase("MergeBinary"))
{
szdirlistfile = args[++nargindex];
}
else if (args[nargindex].equals("-t"))
{
sztype = args[++nargindex];
}
else if (args[nargindex].equals("-j"))
{
numsplitbins = Integer.parseInt(args[++nargindex]);
Expand Down Expand Up @@ -13282,8 +13499,7 @@ else if (args[nargindex].equals("-gzip"))
throw new IllegalArgumentException(szoutputdir+" does not exist and could not be created!");
}
}

Preprocessing.mergeBinarizedFiles(szinputdir, szoutputdir, szdirlistfile, bsplit, numsplitbins, bgzip);
Preprocessing.mergeBinarizedFiles(szinputdir, szoutputdir, szdirlistfile, bsplit, numsplitbins, bgzip, sztype);
}
else
{
Expand All @@ -13293,7 +13509,7 @@ else if (args[nargindex].equals("-gzip"))

if (!bok)
{
System.out.println("usage MergeBinary [-f dirlistfile][-gzip][-splitrows [-j numsplitbins]] inputdir outputdir");
System.out.println("usage MergeBinary [-f dirlistfile][-gzip][-splitrows [-j numsplitbins]][-t type] inputdir outputdir");
}
}
else if (szcommand.equalsIgnoreCase("CompareModels"))
Expand Down Expand Up @@ -13366,7 +13582,7 @@ else if (args[nargindex].equals("-noimage"))

if (!bok)
{
System.out.println("usage CompareModels [-color r,g,b][-noimage] referencemodel comparedir outputprefix");
System.out.println("usage CompareModels [-color r,g,b][-noimage] referencemodelemissions comparedir outputprefix");
}
}
else if (szcommand.equalsIgnoreCase("StatePruning"))
Expand Down Expand Up @@ -14341,6 +14557,7 @@ else if (args[nargindex].equals("-holdcolumnorder"))
else if (args[nargindex].equals("-holdroworder"))
{
bnoorderrows = true;
nstateorder = ChromHMM.STATEORDER_FIXED;
}
else if ((args[nargindex].equals("-printstatebyline"))||(args[nargindex].equals("-printstatesbyline")))
{
Expand Down
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