mlRho version 1.10 commit

On branch master
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   deltaComp.c
	modified:   interface.c
	modified:   interface.h
	modified:   mlComp.c
	modified:   mlRho.c
	modified:   piComp.c
	modified:   profileTree.c
	modified:   profileTree.h
	modified:   rhoComp.c
mlRho version 1.11 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   mlComp.c
	modified:   mlRho.c
mlrho version 1.14 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	new file:   Scripts/pro2sum.awk
	modified:   deltaComp.c
	modified:   interface.c
	modified:   interface.h
	modified:   mlRho.c
	modified:   piComp.c
	modified:   profileTree.c
	modified:   profileTree.h
	new file:   profileTreeBam.c
	modified:   rhoComp.c
	new file:   samtools/AUTHORS
	new file:   samtools/COPYING
	new file:   samtools/ChangeLog.old
	new file:   samtools/INSTALL
	new file:   samtools/Makefile
	new file:   samtools/Makefile.mingw
	new file:   samtools/NEWS
	new file:   samtools/bam.c
	new file:   samtools/bam.h
	new file:   samtools/bam2bcf.c
	new file:   samtools/bam2bcf.h
	new file:   samtools/bam2bcf_indel.c
	new file:   samtools/bam2depth.c
	new file:   samtools/bam_aux.c
	new file:   samtools/bam_cat.c
	new file:   samtools/bam_color.c
	new file:   samtools/bam_endian.h
	new file:   samtools/bam_import.c
	new file:   samtools/bam_index.c
	new file:   samtools/bam_lpileup.c
	new file:   samtools/bam_mate.c
	new file:   samtools/bam_md.c
	new file:   samtools/bam_pileup.c
	new file:   samtools/bam_plcmd.c
	new file:   samtools/bam_reheader.c
	new file:   samtools/bam_rmdup.c
	new file:   samtools/bam_rmdupse.c
	new file:   samtools/bam_sort.c
	new file:   samtools/bam_stat.c
	new file:   samtools/bam_tview.c
	new file:   samtools/bamtk.c
	new file:   samtools/bcftools/Makefile
	new file:   samtools/bcftools/README
	new file:   samtools/bcftools/bcf.c
	new file:   samtools/bcftools/bcf.h
	new file:   samtools/bcftools/bcf.tex
	new file:   samtools/bcftools/bcf2qcall.c
	new file:   samtools/bcftools/bcfutils.c
	new file:   samtools/bcftools/call1.c
	new file:   samtools/bcftools/em.c
	new file:   samtools/bcftools/fet.c
	new file:   samtools/bcftools/index.c
	new file:   samtools/bcftools/kfunc.c
	new file:   samtools/bcftools/kmin.c
	new file:   samtools/bcftools/kmin.h
	new file:   samtools/bcftools/main.c
	new file:   samtools/bcftools/mut.c
	new file:   samtools/bcftools/prob1.c
	new file:   samtools/bcftools/prob1.h
	new file:   samtools/bcftools/vcf.c
	new file:   samtools/bcftools/vcfutils.pl
	new file:   samtools/bedidx.c
	new file:   samtools/bgzf.c
	new file:   samtools/bgzf.h
	new file:   samtools/bgzip.c
	new file:   samtools/cut_target.c
	new file:   samtools/errmod.c
	new file:   samtools/errmod.h
	new file:   samtools/examples/00README.txt
	new file:   samtools/examples/Makefile
	new file:   samtools/examples/bam2bed.c
	new file:   samtools/examples/calDepth
	new file:   samtools/examples/calDepth.c
	new file:   samtools/examples/chk_indel.c
	new file:   samtools/examples/ex1.bam
	new file:   samtools/examples/ex1.bam.bai
	new file:   samtools/examples/ex1.bcf
	new file:   samtools/examples/ex1.fa
	new file:   samtools/examples/ex1.fa.fai
	new file:   samtools/examples/ex1.glf
	new file:   samtools/examples/ex1.glfview.gz
	new file:   samtools/examples/ex1.pileup.gz
	new file:   samtools/examples/ex1.sam.gz
	new file:   samtools/examples/ex1a.bam
	new file:   samtools/examples/ex1b.bam
	new file:   samtools/examples/ex1f-rmduppe.bam
	new file:   samtools/examples/ex1f-rmdupse.bam
	new file:   samtools/examples/ex1f.bam
	new file:   samtools/examples/ex1f.rg
	new file:   samtools/examples/toy.fa
	new file:   samtools/examples/toy.sam
	new file:   samtools/faidx.c
	new file:   samtools/faidx.h
	new file:   samtools/kaln.c
	new file:   samtools/kaln.h
	new file:   samtools/khash.h
	new file:   samtools/klist.h
	new file:   samtools/knetfile.c
	new file:   samtools/knetfile.h
	new file:   samtools/kprobaln.c
	new file:   samtools/kprobaln.h
	new file:   samtools/kseq.h
	new file:   samtools/ksort.h
	new file:   samtools/kstring.c
	new file:   samtools/kstring.h
	new file:   samtools/misc/HmmGlocal.java
	new file:   samtools/misc/Makefile
	new file:   samtools/misc/ace2sam.c
	new file:   samtools/misc/blast2sam.pl
	new file:   samtools/misc/bowtie2sam.pl
	new file:   samtools/misc/export2sam.pl
	new file:   samtools/misc/interpolate_sam.pl
	new file:   samtools/misc/maq2sam.c
	new file:   samtools/misc/md5.c
	new file:   samtools/misc/md5.h
	new file:   samtools/misc/md5fa.c
	new file:   samtools/misc/novo2sam.pl
	new file:   samtools/misc/psl2sam.pl
	new file:   samtools/misc/r2plot.lua
	new file:   samtools/misc/sam2vcf.pl
	new file:   samtools/misc/samtools.pl
	new file:   samtools/misc/seqtk.c
	new file:   samtools/misc/soap2sam.pl
	new file:   samtools/misc/varfilter.py
	new file:   samtools/misc/vcfutils.lua
	new file:   samtools/misc/wgsim.c
	new file:   samtools/misc/wgsim_eval.pl
	new file:   samtools/misc/zoom2sam.pl
	new file:   samtools/padding.c
	new file:   samtools/phase.c
	new file:   samtools/razf.c
	new file:   samtools/razf.h
	new file:   samtools/razip.c
	new file:   samtools/sam.c
	new file:   samtools/sam.h
	new file:   samtools/sam_header.c
	new file:   samtools/sam_header.h
	new file:   samtools/sam_view.c
	new file:   samtools/sample.c
	new file:   samtools/sample.h
	new file:   samtools/samtools.1
	new file:   samtools/win32/libcurses.a
	new file:   samtools/win32/libz.a
	new file:   samtools/win32/xcurses.h
	new file:   samtools/win32/zconf.h
	new file:   samtools/win32/zlib.h
	modified:   stringUtil.c
	modified:   stringUtil.h
	new file:   valgrind.sh
mlRho version 1.15 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   interface.c
	modified:   interface.h
	modified:   mlComp.c
	modified:   mlComp.h
	modified:   mlRho.c
	modified:   profileTree.h
	deleted:    profileTreeBam.c
	deleted:    samtools/AUTHORS
	deleted:    samtools/COPYING
	deleted:    samtools/ChangeLog.old
	deleted:    samtools/INSTALL
	deleted:    samtools/Makefile
	deleted:    samtools/Makefile.mingw
	deleted:    samtools/NEWS
	deleted:    samtools/bam.c
	deleted:    samtools/bam.h
	deleted:    samtools/bam2bcf.c
	deleted:    samtools/bam2bcf.h
	deleted:    samtools/bam2bcf_indel.c
	deleted:    samtools/bam2depth.c
	deleted:    samtools/bam_aux.c
	deleted:    samtools/bam_cat.c
	deleted:    samtools/bam_color.c
	deleted:    samtools/bam_endian.h
	deleted:    samtools/bam_import.c
	deleted:    samtools/bam_index.c
	deleted:    samtools/bam_lpileup.c
	deleted:    samtools/bam_mate.c
	deleted:    samtools/bam_md.c
	deleted:    samtools/bam_pileup.c
	deleted:    samtools/bam_plcmd.c
	deleted:    samtools/bam_reheader.c
	deleted:    samtools/bam_rmdup.c
	deleted:    samtools/bam_rmdupse.c
	deleted:    samtools/bam_sort.c
	deleted:    samtools/bam_stat.c
	deleted:    samtools/bam_tview.c
	deleted:    samtools/bamtk.c
	deleted:    samtools/bcftools/Makefile
	deleted:    samtools/bcftools/README
	deleted:    samtools/bcftools/bcf.c
	deleted:    samtools/bcftools/bcf.h
	deleted:    samtools/bcftools/bcf.tex
	deleted:    samtools/bcftools/bcf2qcall.c
	deleted:    samtools/bcftools/bcfutils.c
	deleted:    samtools/bcftools/call1.c
	deleted:    samtools/bcftools/em.c
	deleted:    samtools/bcftools/fet.c
	deleted:    samtools/bcftools/index.c
	deleted:    samtools/bcftools/kfunc.c
	deleted:    samtools/bcftools/kmin.c
	deleted:    samtools/bcftools/kmin.h
	deleted:    samtools/bcftools/main.c
	deleted:    samtools/bcftools/mut.c
	deleted:    samtools/bcftools/prob1.c
	deleted:    samtools/bcftools/prob1.h
	deleted:    samtools/bcftools/vcf.c
	deleted:    samtools/bcftools/vcfutils.pl
	deleted:    samtools/bedidx.c
	deleted:    samtools/bgzf.c
	deleted:    samtools/bgzf.h
	deleted:    samtools/bgzip.c
	deleted:    samtools/cut_target.c
	deleted:    samtools/errmod.c
	deleted:    samtools/errmod.h
	deleted:    samtools/examples/00README.txt
	deleted:    samtools/examples/Makefile
	deleted:    samtools/examples/bam2bed.c
	deleted:    samtools/examples/calDepth
	deleted:    samtools/examples/calDepth.c
	deleted:    samtools/examples/chk_indel.c
	deleted:    samtools/examples/ex1.bam
	deleted:    samtools/examples/ex1.bam.bai
	deleted:    samtools/examples/ex1.bcf
	deleted:    samtools/examples/ex1.fa
	deleted:    samtools/examples/ex1.fa.fai
	deleted:    samtools/examples/ex1.glf
	deleted:    samtools/examples/ex1.glfview.gz
	deleted:    samtools/examples/ex1.pileup.gz
	deleted:    samtools/examples/ex1.sam.gz
	deleted:    samtools/examples/ex1a.bam
	deleted:    samtools/examples/ex1b.bam
	deleted:    samtools/examples/ex1f-rmduppe.bam
	deleted:    samtools/examples/ex1f-rmdupse.bam
	deleted:    samtools/examples/ex1f.bam
	deleted:    samtools/examples/ex1f.rg
	deleted:    samtools/examples/toy.fa
	deleted:    samtools/examples/toy.sam
	deleted:    samtools/faidx.c
	deleted:    samtools/faidx.h
	deleted:    samtools/kaln.c
	deleted:    samtools/kaln.h
	deleted:    samtools/khash.h
	deleted:    samtools/klist.h
	deleted:    samtools/knetfile.c
	deleted:    samtools/knetfile.h
	deleted:    samtools/kprobaln.c
	deleted:    samtools/kprobaln.h
	deleted:    samtools/kseq.h
	deleted:    samtools/ksort.h
	deleted:    samtools/kstring.c
	deleted:    samtools/kstring.h
	deleted:    samtools/misc/HmmGlocal.java
	deleted:    samtools/misc/Makefile
	deleted:    samtools/misc/ace2sam.c
	deleted:    samtools/misc/blast2sam.pl
	deleted:    samtools/misc/bowtie2sam.pl
	deleted:    samtools/misc/export2sam.pl
	deleted:    samtools/misc/interpolate_sam.pl
	deleted:    samtools/misc/maq2sam.c
	deleted:    samtools/misc/md5.c
	deleted:    samtools/misc/md5.h
	deleted:    samtools/misc/md5fa.c
	deleted:    samtools/misc/novo2sam.pl
	deleted:    samtools/misc/psl2sam.pl
	deleted:    samtools/misc/r2plot.lua
	deleted:    samtools/misc/sam2vcf.pl
	deleted:    samtools/misc/samtools.pl
	deleted:    samtools/misc/seqtk.c
	deleted:    samtools/misc/soap2sam.pl
	deleted:    samtools/misc/varfilter.py
	deleted:    samtools/misc/vcfutils.lua
	deleted:    samtools/misc/wgsim.c
	deleted:    samtools/misc/wgsim_eval.pl
	deleted:    samtools/misc/zoom2sam.pl
	deleted:    samtools/padding.c
	deleted:    samtools/phase.c
	deleted:    samtools/razf.c
	deleted:    samtools/razf.h
	deleted:    samtools/razip.c
	deleted:    samtools/sam.c
	deleted:    samtools/sam.h
	deleted:    samtools/sam_header.c
	deleted:    samtools/sam_header.h
	deleted:    samtools/sam_view.c
	deleted:    samtools/sample.c
	deleted:    samtools/sample.h
	deleted:    samtools/samtools.1
	deleted:    samtools/win32/libcurses.a
	deleted:    samtools/win32/libz.a
	deleted:    samtools/win32/xcurses.h
	deleted:    samtools/win32/zconf.h
	deleted:    samtools/win32/zlib.h
mlRho version 1.16 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   mlComp.c
	modified:   mlComp.h
	modified:   mlRho.c
	modified:   profileTree.c
	modified:   profileTree.h
	modified:   valgrind.sh
mlRho version 1.19 commit
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   mlComp.c
	modified:   mlRho.c
	modified:   profileTree.c
	modified:   profileTree.h
	modified:   stringUtil.h
	deleted:    test.pro
	modified:   valgrind.sh
mlRho version 1.21 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   interface.c
	modified:   interface.h
	modified:   mlRho.c
	modified:   profileTree.c
	modified:   profileTree.h
	modified:   valgrind.sh
mlrho version 1.23 commit

	modified:   Makefile
	renamed:    TestMlPi/Makefile -> SimPro/Makefile
	renamed:    TestMlDelta/eprintf.c -> SimPro/eprintf.c
	renamed:    TestMlDelta/eprintf.h -> SimPro/eprintf.h
	renamed:    TestMlDelta/interface.c -> SimPro/interface.c
	renamed:    TestMlDelta/interface.h -> SimPro/interface.h
	renamed:    TestMlDelta/ranNum.c -> SimPro/ranNum.c
	renamed:    TestMlDelta/ranNum.h -> SimPro/ranNum.h
	new file:   SimPro/simPro.c
	renamed:    TestMlDelta/testMlDelta.c -> SimPro/testMlDelta.c
	deleted:    TestMlDelta/Makefile
	deleted:    TestMlPi/README
	deleted:    TestMlPi/eprintf.c
	deleted:    TestMlPi/eprintf.h
	deleted:    TestMlPi/interface.c
	deleted:    TestMlPi/interface.h
	deleted:    TestMlPi/ranNum.c
	deleted:    TestMlPi/ranNum.h
	deleted:    TestMlPi/testMlDiv.c
	deleted:    TestMlPi/testMlPi.c
	modified:   deltaComp.c
	modified:   interface.c
	modified:   interface.h
	new file:   ld.c
	new file:   ld.h
	modified:   mlComp.c
	modified:   mlComp.h
	modified:   mlRho.c
	new file:   pairs.h
	modified:   piComp.c
	new file:   profile.c
	new file:   profile.h
	modified:   profileTree.c
	modified:   profileTree.h
	deleted:    queue.c
	deleted:    queue.h
	deleted:    rhoComp.c
	deleted:    tab.c
	modified:   valgrind.sh
mlrho version 1.23 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   deltaComp.c
	modified:   eprintf.h
	modified:   interface.c
	modified:   interface.h
	modified:   mlComp.c
	modified:   mlComp.h
	modified:   mlRho.c
	modified:   piComp.c
	modified:   profileTree.c
	new file:   queue.h
	modified:   valgrind.sh
mlrho version 1.25 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   mlRho.c
	modified:   piComp.c
	modified:   valgrind.sh
mlrho version 2.0 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	new file:   Scripts/bam.sh
	new file:   Scripts/bam2pro.awk
	new file:   Scripts/sim.sh
	deleted:    SimPro/Makefile
	deleted:    SimPro/eprintf.c
	deleted:    SimPro/eprintf.h
	deleted:    SimPro/interface.c
	deleted:    SimPro/interface.h
	deleted:    SimPro/ranNum.c
	deleted:    SimPro/ranNum.h
	deleted:    SimPro/simPro.c
	deleted:    SimPro/testMlDelta.c
	modified:   mlRho.c
	deleted:    pairs.h
	modified:   profileTree.c
	deleted:    queue.h
	deleted:    tab.h
mlrho version 2.1 commit

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   ld.c
	modified:   mlRho.c
	modified:   piComp.c
	modified:   profile.c
	modified:   profileTree.c