Merge pull request #191 from gymrek-lab/newtool-mosaicSTR

Newtools prancSTR and simTR

.github/workflows/tests.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Install test dependencies
         shell: bash -el {0}
         run: |
-          mamba install -c conda-forge -c bioconda bcftools pip pytest pytest-cov
+          mamba install -c conda-forge -c bioconda bcftools pip pytest pytest-cov art
       - name: Upgrade pip and install our package
         shell: bash -el {0}
         run: |

.readthedocs_conda_env.yml

@@ -19,3 +19,4 @@ dependencies:
   - cyvcf2
   - sphinx_rtd_theme
   - statsmodels
+  - pyfaidx

README.rst

@@ -74,7 +74,9 @@ checkout the branch you're interested in, and run the following command from the
 
 Note: required package :code:`pybedtools` requires zlib. If you receive an error about a missing file :code:`zlib.h`, you can install on Ubuntu using :code:`sudo apt-get install zlib1g-dev` or CentOS using :code:`sudo yum install zlib-devel`.
 
-Note: make sure TRTools is not installed in the environment via a different method before installing from source. :code:`which dumpSTR` should return nothing
+Note: make sure TRTools is not installed in the environment via a different method before installing from source. :code:`which dumpSTR` should return nothing.
+
+Note: if you will run or test :code:`simTR`, you will also need to install `ART <https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm>`_. The simTR tests will only run if the executable :code:`art_illumina` is found on your :code:`PATH`. If it has been installed, :code:`which art_illumina` should return a path.
 
 Tools
 -----
@@ -86,6 +88,8 @@ TRTools includes the following tools.
 * `statSTR <https://trtools.readthedocs.io/en/latest/source/statSTR.html>`_: a tool for computing various statistics on VCF files
 * `compareSTR <https://trtools.readthedocs.io/en/latest/source/compareSTR.html>`_: a tool for comparing TR callsets
 * `associaTR <https://trtools.readthedocs.io/en/latest/source/associaTR.html>`_: a tool for testing TR length-phenotype associations (e.g., running a TR GWAS)
+* `prancSTR <https://trtools.readthedocs.io/en/latest/source/prancSTR.html>`_: a tool for identifying somatic mosacisim at TRs. Currently only compatible with HipSTR VCF files. (*beta mode*)
+* `simTR <https://trtools.readthedocs.io/en/latest/source/simTR.html>`_: a tool for simulating next-generation sequencing reads from TR regions. (*beta mode*)
 
 Type :code:`<command> --help` to see a full set of options.
 
@@ -139,7 +143,7 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 
 1. Consider `discussing <https://github.com/gymrek-lab/TRTools/issues>`_ your solution with us first so we can provide help or feedback if necessary.
 #. Install TRTools from source `as above <From source_>`_.
-#. Additionally, install :code:`pytest`, `pytest-cov <https://anaconda.org/conda-forge/pytest-cov>`_ and :code:`sphinx>=3` in your environment.
+#. Additionally, install :code:`pytest`, `pytest-cov <https://anaconda.org/conda-forge/pytest-cov>`_, :code:`sphinx>=3` and :code:`sphinx_rtd_theme`, in your environment.
 #. Fork the TRTools repository.
 #. The :code:`develop` branch contains the latest pre-release codebase. Create a branch off of :code:`develop` titled with the name of your feature.
 #. Make your changes. 

RELEASE_NOTES.rst

@@ -1,3 +1,11 @@
+5.1.0
+-----
+
+New features:
+
+* Added prancSTR for mosaicism detection
+* Added simTR for simulating NGS reads with stutter errors at TRs
+
 5.0.2
 -----
 

doc/UTILITIES.rst

@@ -14,6 +14,8 @@ TRTools offers a variety of command-line tools for performing manipulations to T
    source/compareSTR.rst
    source/mergeSTR.rst
    source/associaTR.rst
+   source/prancSTR.rst
+   source/simTR.rst
 
 .. Include directives from tool READMEs
 
@@ -41,6 +43,14 @@ TRTools offers a variety of command-line tools for performing manipulations to T
    :start-after: overview_directive
    :end-before: overview_directive_done   
 
+.. include:: ../trtools/prancSTR/README.rst
+   :start-after: overview_directive
+   :end-before: overview_directive_done   
+
+.. include:: ../trtools/simTR/README.rst
+   :start-after: overview_directive
+   :end-before: overview_directive_done   
+
 :doc:`source/dumpSTR`
 
 * |dumpSTR overview|
@@ -64,3 +74,12 @@ TRTools offers a variety of command-line tools for performing manipulations to T
 :doc:`source/associaTR`
 
 * |associaTR overview|
+
+:doc:`source/prancSTR`
+
+* |prancSTR overview|
+
+:doc:`source/simTR`
+
+* |simTR overview|
+

doc/source/prancSTR.rst

@@ -0,0 +1 @@
+.. include:: ../../trtools/prancSTR/README.rst

doc/source/simTR.rst

@@ -0,0 +1 @@
+.. include:: ../../trtools/simTR/README.rst

doc/trtools.prancSTR.rst

@@ -0,0 +1,5 @@
+trtools.prancSTR module
+---------------------------
+
+.. automodule:: trtools.prancSTR
+  :imported-members:

doc/trtools.simTR.rst

@@ -0,0 +1,5 @@
+trtools.simTR module
+---------------------------
+
+.. automodule:: trtools.simTR
+  :imported-members:

example-files/CBL.fa

@@ -0,0 +1,2 @@
+>chr11_CBL
+GTAAAATGAGGCTGAGAACTACTGGGCTGTGTTCCCAGAAGGTTAAGGCATTCTAAGTCACAGGATGAGATAGGAGGTTGGCACAAGATACAGATCATAAAGACCTTGCTGATAAAACAGGTTGCAGTAGAGGAGCTGGCCAAAACCCACCAAAACCAAGATGGCGACGAGAGTGACCTCTGGTCGTCCTCGCTGCTGCACTCCCACCAGCGTCATCACAGTTTACAAATGCCATGGCAACATCAGGAAGTTACCCTGTATGGTGTAAAAAGGGGAGGCATGAATAATCCACCCCTTGTTTAGCATATCATCAACAAATAACCATAAACATGGTTATGTCTATGGAGTCACCATCCTTTTATTCCAACACTTTCCTAATAAACTTGTTTTCACTTTACTCTATGGAGTTGCCCTGAATTCTTTCTTGTGCGAGATCCAAGAACCCTCTCTTGGGATCTGGATCAGGACCCCTTTCCTGTAACAAAAGTGCTGGGATTGCAGGCATGAGCCACTGCGCCCAGCAAATTTTTGTATTTTTTATAGAGACAGGGTTTTGCTATGTTGCCCATCCTGGTCTCGAACTCCTGGGCTCAAGCAATCCATCTGCCTCAGCCTCCCGAAGTGCTGGGACTACAGGCAGGAGCTACCTTGCTTGGTCTGGGAACTTTTTTCCCATGGAATGATTACTGTCCCCATTATACTTGTTAACATAAAGGAAAAAACTGGCACAAATTTAAGTAGAGAGTTTACTTGGACCAATTTTGAGGACAGCAATCCAGGAGCGTAGATTCAAGTTGCCCTGGACAATAGGCTCAGATTATCAGATTAATAGCAGTTACAAACGTGTGTGGGGTTTTTTTTTTTTTTTTTTTTTTGAGATGGCGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAACCTCTGCCTCCTGATTCAAGTGATTCTCCCGCCTCAGCCTCCCGAGTAGCTGAGATTACAGGCGCCCACCACCACGTCCGGCTAATTTTTTGTATTTGTAATAGAGTCAGCGTTTCGCCATCTTGGCGAGGCTGGTCTTGAACTCCTGATCTTGTGATCCGCCTCCCAAAGTGCTGAGATTACAGGCCTGGCCAACAAGTGTGTTTTTAAAGGAAAAAAGAGGCCAGGTGTGGTGGCTCATGCCTGTAATCTTAGCACTTTGGGAGGCCCAGGCAGGAGGATAGCTTGAGGCCAGGAATTTAAGATCAGCATGGGCAACTTGCGACTACCACCACCCCACCGAAAATAAATAAATAAATAAATAAATAGAAGAGGCAGTTCCTAAACTGTTTGCCAATCACTTACATTAACACAGCGTAAGGTATTTGATTGGCTGTACGTTGTTCTTTGTGTCACAGATTCCACGAACATGAAGATAATGGGTGAGGCAGCTAGTCAGGGACCAAATGCCTTTAAACCATTGCCCCCAGGCATGGGTCGGGGATTTGTGACTGAAGTCCCATACTCATGTCTCGCTGGGCCTGATAATTTTGCATACCTCACATAGTTCAGACTGCTTTAAGCTATTTTTCTTTTCTCATCCTGATGCATAGAATGATATTAGAATAGAGATTGCAGAATACAAGCAACTATACCTCAGAAGAGAATATAGTTTCCAAATACGTTCAGTCAATGGACTTTCCTTTTTTTGTTTTGAGATGGAGTCTCGCTCTGTGCCCAGGCTGAAGTGGAGTGGTGCGATCTCGGATCACTGCAACCTCTGCCTCCCAGGTTCAAGGCATTCTCCTGTCTCAGCTTCCAGAGTAGCTGGGATTACAGGTGCCCACCACCACGCCTGGTTAATTTTTGTATTTTAGTAGAGACGGGGTTTCGCCACGTTGGTCAGGTTGGTCTCAAACCCCTGACCTCAGTTGATCCGCCCGCCTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGTGCCCGGCCCAGTCAATGGACTTTCAGGTGCAGAATGAGGATGTGGTTTGGGGTGAAGGTGAAGTGGGATAAGAAAAAGGCTACATGTTACACGATGTGATGCAGGATGAACCAACTCTAGCATAATCCAGAATGGGAATGACATTGTGATCAACAGTCCAACCCCCTCTCTTGTACATTTTCTAAAGCAAGCGAAATAAAAATTGTGGCAGGGCACGGTGGCTCACGCCTATAGTCCTAGCACTTTGGGAGGCCGAGGTGGGTGGATTGCCTGAGCTCAGGAGTTTGAGATCAGCCTGAGCAACACGGTGAAACCCTGTCTCTATTAAAATACAAAAAATTAGCTGGGCATGGTCTCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCTTGAACCCGAAGTGGAGGTTGCAGTGAGCCAAGATTGCACCACTGTACTCCAGCCTGGGTGACAGAGCGAGACTCTGTTTCAAAGAAAAAAAAAAGGTAAAAAAAAGGGTAATCTTCCTTTTCTTATTAACTTTATTTATTTATTTGTTTATTTATGTTTTTGAGACAGAGTCTCACTCTTGTCGCTCAGCCTAGAGTGCAGTGGCACAATCTGGGCTCACTGCAACTTCTGGCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGTGCGCCACCACACCCAGCTATTTTTTTTGTATTTTTAGTAGAGATGGGGTCTCACCATGTTGGCCAAGGATGGTCTCGATCTCCTGACCTCGTGTCCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTCATTTTTTTATTTTTAGTAAAGACAAGATTTCACCATGTTGGCCAAGCTGGTCTCCAACTCCTGACCTGAGGTGATCCGCCTCCCTCGGCCTCACAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCTGGGCCGAATGGATTGGATTTTAAAGCATACTTCAGGCAGATGGAATAAGGGAATAGTCTGAGTAACGGTGATGAGAAAAGAAAGAATTGGCCAGGTGCGGTGGCTCACACCCATGATCTCAGCACTTTGGGAGGCTGAGGAGGGCAGATCCCCTCAGGTCAGGAGTTGAAGACCAGCTTGGCCAACATGGTGAAATCTCATCTTTACTAAAAATACAAAAATTAGTCAGGTGTGGTGGCGGGCACTTGTAATCCCAGCTACTCGGGGGGCAGAAGTTGCAGTGAGCCAAGATTGTGCCACTGCACTCCAGCCTGGGTGACAGACTCTGTCTCAAAATAAAATAAAATAAATAAATAAATAAAAAAGAAATAATTGTATTTGATGACTTGGTGAGTCAGCTAGCATAAGACATGTGTACCAGGGAGTAGTATAAAACTACAAGGTTGTTTAGCTTGGAGTTAGAGCAACTTGTCAATTTTATTCCCGAGGCAATGGGAGGTGTTTAAAGTTTTTTTGCGATGCTGTCTGAACTATACTTTAGGAAGCCTATGGTGGCAGGATGAATTGAAGGCACAGGAAAAGGTTTCAATATTCAATAGTCCAGGGAAAAGAAACGGAGGACCTGCAACTAGGTGTTGGCACTAAGGGATGGAGCTTTGCCTAGATTTTCCCTTTGTAGATTCTTCTCTTCCTGGATGGAAAATGATAAAAGGAAATTCTTCTGATAGTAAATTATAATGTTGACTCCAAAATCAATTCTAGATAAAGGCGATTAAATTGCAAACCCAGGATGCCTGTCTGAATGGTCCCTGCATTCAAAGATATTTTCCCCTTTACAGGAGCACCGGATAAATTTAACTCCCTAATCTGTCAAGGGCTTTGTGGAAGAGCCTGGAGGGGGATCGAAGGCGGAACTGATACTGACACACCTGGGTCTGCAAACTCCCAAAACTGAGGCTCAGAATTAGTAAATTAGGGCAGGGCACTTCCCTCTTTGGAAGGGAAGTTCCTATTTTCAAAGTTCTTCCAACGGAACTTTTACATTAGAGAAGTGTAATTGACTGAGAAGTGGAAGTGACCAGGAACAGCATTTCTGTTCCCTGGGCGGGAGAGAGAACCCCCTCGGGCGGAGCCAGCAGCAGGTCAGCTTCTGAGGGGGCCCTCATGCTGGCGGCGCCGACCTGTGGTGCAATGCTCTGAGTAGGAGAATCTTAAATACATGTTTGAGATTCAATTCCCAGAAACGTAACTAGTCTTCACAAGCCAAAAAAATAAAAATAAAAAATAAAAAAAGGAAGTGATTTCTTTTCAAGAGGTCAAAGGGCCTGGAAGAAGAGGTCCTGGCTTGAGTGTCTCAAGGCTTTCTGGGGCCTAATCCGGCTGGAATGGGCCGCAGCATTCATATTCCTGTCCTTGGTCGTGTCTTAATGAAGAATTGAAAATAATAAGGGGTGGAGAAATAACTTTCCTTTTTCTCCCACCATCCTCCCACAGTGTAAATAAACAAATAACTCTAAGCTCGATTTCCTCATTTGTCAGGGGTGGGGAAAGACTTGACATCAGGACTCTTCCATTCCATCGCCACCTGTCTTAATTTAAACATTCCCATGACCCACCCCAGAAGCGCCAACCTCCCGCCCACAAGGAGCATGGAAGTCTTGGTTTCTGGCTACTGCGCAGACTCCACCTTGGACCTACTCCCCAACCCCCCGCCGCTCCTTTCCCCGTTTCTCCAGCAGAGGGCGCAGGCCCAAAGGTTCCGCCGACCCCGCCCCAGCCTGGCCCCGCCCCGCCCCGGCGTAGGGGCGGGGAAGACGGGCACAGAAACCTGGCCGCGGCTTTCCGGGAGCTGTGGGCACGCGAGCTGCTCGAAGCCGGTGGCCCGGGGATCGTCGCTGCCCAGTCCGGCCGCGGCCGGCCGCTTCCCCGAGCTTACCAGTAAGCCGGTCCGCCTCCGGGACGCGCCCCGCCCGCCCCGGGCTCGCGCGCTCTGAAGGGGCGCGTCCCGCGCACTCCCGGCGCCGCCCACTCCCCTCCCCACGGCCGCTCCTCCCTCCGCCCGGATAGCcggcggcggcggcggcggcggcggcggcggcggCCGGGAGAGGCCCCTCCTTCACGCCCTGCTTCTCTCCCTCGCTCGCAGTCGAGCCGAGCCGGCGGACCCGCCTGGGCTCCGACCCTGCCCAGGCCATGGCCGGCAACGTGAAGAAGAGCTCTGGGGCCGGGGGCGGCAGCGGCTCCGGGGGCTCGGGTTCGGGTGGCCTGATTGGGCTCATGAAGGACGCCTTCCAGCCGCACCACCACCACCACCACCACCTCAGCCCCCACCCGCCGGGGACGGTGGACAAGAAGATGGTGGAGAAGTGCTGGAAGCTCATGGACAAGGTGAAAGGCCGGCTGAGCGCCCGCTGTTGCAGGGTGGGCGTGGGCGGAGGGCCGCGGGGAGGGGAACGAGCGGACGGAGGAAGCGGGGGAGGGGACGGGTCTGGTGAAGCCGGGGAGGCGCGGAGCCGGGGTGACCGGCCGGGGGCGTGGGGGCAGGGACGAGGCCGGGAGGGTGGGGGGCGGCGTGGGGGAGGGGCTGCCGTTGGGAGTCGGGGAACGCTGGGGTGCCGCGTTTGGGGTAGCCAGACAAAGATGGAGTGGGGGCTGGGGCGAAGGTTAACTGGGAAGTCAGTGGGGCGGAAGTACAATGAGGGGTGCGGAGTTTGGGGCTCTGTGCAGGGTGTAGGGATGTAGGTCACGGAATTGGCCTGGGAGGTTAGCAGGGAGGGGGTGAGGAAGAGTGATGTACCGGCTGGGGCTCTTGGCTGGGTGAGATCTGACTAGGGAATTAGGTTCATGGGCTCTGACTGAGGAACCTGGCTGGGGTCAGGACAGCTCTCAGGGAAGCTGTGCTCTGGGTGAGAGTATAGTCCTTTCTCATTAAGATGTAACACGAAGATAAAAGACATATTGATGTTTAAGTGAGGCAAGGAAAGAACTTTCCTCCCCATCTAGCGCCGGCTCAAGTTTTTTGTTACCCTCAGAAACACTGGATGTGATCCATTGCTGGTGCTGAGATATGCACTGATTAAACCACAAGTTCTGGTTAGAACTATTATCTTCTGAAAGATGGACTGGCTGAGCCTGTTAAGCAGCAGCAGATTCTGACTTCTTAATAACTTCCTCCCTACTACATCGCTTGAGCTGGGTTCTTTTTTTCTGGTAACGGTTCTGACTCCTTATTACAGGTCCTGACTTTAAACTTGTTCGTTGAGCTTCTTTGATTACGCTTTTTTGTTTGTTTGCTTTTTGCAAGTGCGAACAAAAATAACTCCTTTATATTTAGCCACTAAGTTTGTCATTTGGGAGAATTTTACTTCCTTATAGTTGTGTCTATATGATGAAATGTAGTCAGTCTCAAGTATTTAACTGTTTAAGCAGTCGGACGCTTTGTCAGAATTCAATACGTTTTCTTGGTATTTTTCATATTCTTTAATTAATTACTTTGACAAAATTCATATTGCGTATGAAAAGTGATTAGAAGTATCTGGCACGTTTTAAGAGAATGGTGTTATTTCCTCCAGGGTAAAATTTGGTTTTCTTTGGTTCCTCCCTGGGCCTCGGTTCCTCTTCTGTAAAGTTCTTCATGGGTTGCTTTGGACTAGAAACCGCTAATAAAATGATTATGAAGCACTTAGCCAATGTAATGTGCAATTTAAATGCTTAATAAGTCCTGTGTGTGAATTAACACTCCAGTAGTGCATGCCAGTGGTTTCATAGCCACCTTTTTAGGGCTGGCTTTTCTCATGTTAAATAATTGGTATTGTAATTAATGACACAAGTATTCGTGTGTTGATTATATTGGTGGTGTAGTACTAATTTTATTGTTAGAAATTATAATAAAATCCTTACAGAAAGTTTAGGTGTGTAAAGGAAACTTTAAATGTGTCGACTCCTTTAAAAAAAACACATCGAAGATATTCAAATGCTAAAGTTTGTTAGTTTGCTTTTTAGGGATTTATCGTTAAGGACTACAAATTTTACTCTGGCATAGAAAAAATACTTTTCTAATGAGTGTCTCGTATCAGACATGTGGGTGCAGTACAATCAAAATTGTGTTGATTAGTGGCCTCTGCTTAAGAATAATCTGTTTACTAAAGAGTTTCTGTATTCTGTATTCTTTTTTTTTTTTTGAGACGGAGTTTTTCGCTCTTGTTACCCAGGCTGGAGTGCATGGTGCGATCTCGACTCACTGCAACCTCCGCCTCCTGGGTTCAAGACATTCTCGTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGCGCGCCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCATCATGTTGACCAGGCTCGTCTCGAACTCCTGACCTCAGGTGATCCATGCGCCACGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGGGCCTGGCCCTGTATTCTTAAAGAATAAGAGTATTCTGTATTCTTATTAAAGTGTTTCTATAAATACAGAGTAAGTTGTAGATAGTCCTATTCTACAAGGTAGCCCAAATAAAATCCTCCCTTAAGTCTTACTCCTTCATCTATTTAAAGTATGTGTATTGAATTTTGATTTATTCTGCAGAATGTTTAATTATTTGGGAAGAATAAAGAGGACTCAAAGTTTAGACTCAAATTGCTTTTCAGGTTTGATAGTTTCACGGAAAGTAGGCTTCTAGCTTTTCCCTTCCAGTGTAGGGAGAGGGATGTTTTATTTTTGTATTACTTGCCTCGGAAGTTGATTTTAATACTGTCTGTTCCCCTCTTATCACGTATTTCTAGTTGCTCTGAAAACGTAGTACTTTCTAATGTGTTAGTCTGATACGTTTATACTGCTTTCCAGATTTTCTGAATACCTCTGTGATGTTACTAGATTGCACCATCTCTTTTACCCTTGATGTTTTGAGCATAAGGTGTCCTCTTTTTTCACTTTATTTTTATTGTTGAAAGTCTTAAATGTGTCACCACACCTTGACTTCATGTGCTATAAGTGGTGAAGAACCTACTGTCAAATCCACAGATGTCCCACACATTTAATTCTTTTTAACAAAATTTCTGGGCCGGGCCCCGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGCTCACTTGAGGTCAGGAGCTCCAGACCAGCTCTGCCAACATGGTGAAATGCTGCCTCTACTAAAAAATACAAAAATTAGCTGGGTGTGGTGGCAGACGCCTGTAATCCCAGCTACTTGGGAGACTGGGACAGGAGAATCCCTTGAACCTGGGGCAGAGGTTGCAGTGAGCCAAGATCGCACCACTGCACTCTAGCCTGAGCGACAGAGTGAGACTCCGTCTCAAAAAAAAAAAAAAGTCTGTTTAATTCTTTTAAATGACACACATTTAGTTCTAAGTCACCATCTCATACCTGCTTTATCTTTGTTGTTGAAGCTGGATGAATATTATTCCAGCCAACTCTTAATCAGTTTATTGAATTAGCACTGGGAGCTGTTAGTCTCTTTCCTTCCCCCAATATTGGATATATACAGATGGAAAAAGTTGGCATAAGTCATGGGTTCTGGTTAACATAGGCCCGATTTACTAATCCATTATGGAACTTAAACTTAACTGTTGGAAAAATGTTTGTGCTAGAATGCTTGTTATTAAACAAAAGTTAGACAGAGCCACTGGTTTTCTTTTTGCCACCCCAGGATATTGTAATAAACATGTGCATAAATACTTGTATGTGAAGTGGCTTGTAAGCCAAAAGACAATTAGGCAGGGAGGAGAGGAGTGGGAAGTGGAGAGAAAAGAGAAAAAGTCACCTAAATTGGCCTTAAATGTATGCTGGGCTCACACCTGTAATCCCAACACTTTGGGAGGATGAGGTAGGCAGATCATTTGATCCCAGCTTCAGCCCAGGAATTCCAGACCAGCCTGGGCAACATGACGAAACCCTGTCTCTACAAAAAATACACATATTAGCCAGGCGTGGTGGTGCCTTCCTCTAAGCTCGAGCTGCTTGGGAGGATCACTTGAGCTTGGGAGATAGAGGCTGCAATGAGCTGTTGAGTCAGCCACTGCACTCCAGCCTGGGCAACAGAGTGACACCCTGTTTCAAAAACAAATAAATTGCTTTAAATGTAAATTTAAAAGTATCAAAGTGTTTAATTTAGTAAGAGACTTTATTTATTTATTTATTTGCTCTGTCACCCAGGCTGGAATGCAGTGGCATGATCTCGGCTCATTGTTTCCTCTACCTCCCAGGTTCAAATGATTTTCGTGCCTCAGCCACCAAGTAGCTGGGATTATAGGCATGCGCCACCACACCTGGCTAATTTTTCAATTTTTTTTTTTTTTTTTTTTTTTTTACTAGAGACGGATTTTCACCATGTTGGCCAGGCTGCTCTCGAACTCCTGGCCTCAATTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGAGGTGGGATAACAGGCATGAGCCACCGCGCCTGGCTCAATTTAGTAAGAGACTTTAAATTCCATTATGAAATAGAACAGAGGTTGGCAAACTTTTTCTGTAAAGGGAGGTTTCAGGGCCACTGTAAATACAGTAATCCTCCATTATTCTAGGGGATATGTTCAAGACACCCAGTGGATGCCTGAAAACCCCCAATAGTACTGAACCGTGTACATATACTATGTTTTTCCTATACATACCTACCTATGATAAAGCTTAATTTATAAATTAGGCACAGTGAGAGATTAACAACAACAATAATGAAAGAGTACAATTACAAAATACACTGTAGTAAAAGTTATATAAATGTAGTCTTCCAAAATATCTTATTGTAGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAAGCGGATCATCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAAAAAGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCCGGGCATGGTGGTGGGTGCCTGTAATCCCAGCTACTTGAGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGA

example-files/CBL.fa.fai

@@ -0,0 +1 @@
+chr11_CBL	10033	11	10033	10033