diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/MANIFEST.in b/MANIFEST.in old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/c-sandbox/obicount/Makefile b/c-sandbox/obicount/Makefile old mode 100644 new mode 100755 diff --git a/c-sandbox/obicount/obicount.c b/c-sandbox/obicount/obicount.c old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/__init__.py b/distutils.ext/obidistutils/__init__.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/__init__.py b/distutils.ext/obidistutils/command/__init__.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build.py b/distutils.ext/obidistutils/command/build.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_cexe.py b/distutils.ext/obidistutils/command/build_cexe.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_ctools.py b/distutils.ext/obidistutils/command/build_ctools.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_exe.py b/distutils.ext/obidistutils/command/build_exe.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_ext.py b/distutils.ext/obidistutils/command/build_ext.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_files.py b/distutils.ext/obidistutils/command/build_files.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_scripts.py b/distutils.ext/obidistutils/command/build_scripts.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/build_sphinx.py b/distutils.ext/obidistutils/command/build_sphinx.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/install.py b/distutils.ext/obidistutils/command/install.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/install_scripts.py b/distutils.ext/obidistutils/command/install_scripts.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/install_sphinx.py b/distutils.ext/obidistutils/command/install_sphinx.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/littlebigman.py b/distutils.ext/obidistutils/command/littlebigman.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/pidname.py b/distutils.ext/obidistutils/command/pidname.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/command/sdist.py b/distutils.ext/obidistutils/command/sdist.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/core.py b/distutils.ext/obidistutils/core.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/dist.py b/distutils.ext/obidistutils/dist.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/__init__.py b/distutils.ext/obidistutils/serenity/__init__.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/bootstrappip.py b/distutils.ext/obidistutils/serenity/bootstrappip.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/checkpackage.py b/distutils.ext/obidistutils/serenity/checkpackage.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/checkpython.py b/distutils.ext/obidistutils/serenity/checkpython.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/checksystem.py b/distutils.ext/obidistutils/serenity/checksystem.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/globals.py b/distutils.ext/obidistutils/serenity/globals.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/rerun.py b/distutils.ext/obidistutils/serenity/rerun.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/snake.py b/distutils.ext/obidistutils/serenity/snake.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/util.py b/distutils.ext/obidistutils/serenity/util.py old mode 100644 new mode 100755 diff --git a/distutils.ext/obidistutils/serenity/virtual.py b/distutils.ext/obidistutils/serenity/virtual.py old mode 100644 new mode 100755 diff --git a/distutils.ext/src/littlebigman.c b/distutils.ext/src/littlebigman.c old mode 100644 new mode 100755 diff --git a/distutils.ext/src/pidname.c b/distutils.ext/src/pidname.c old mode 100644 new mode 100755 diff --git a/doc/.gitignore b/doc/.gitignore old mode 100644 new mode 100755 diff --git a/doc/Doxyfile b/doc/Doxyfile old mode 100644 new mode 100755 diff --git a/doc/Makefile b/doc/Makefile old mode 100644 new mode 100755 diff --git a/doc/conf.py b/doc/conf.py old mode 100644 new mode 100755 diff --git a/doc/source/DMS.rst b/doc/source/DMS.rst old mode 100644 new mode 100755 diff --git a/doc/source/UML/OBIDMS_UML.png b/doc/source/UML/OBIDMS_UML.png old mode 100644 new mode 100755 diff --git a/doc/source/UML/OBITypes_UML.class.violet.html b/doc/source/UML/OBITypes_UML.class.violet.html old mode 100644 new mode 100755 diff --git a/doc/source/UML/OBITypes_UML.png b/doc/source/UML/OBITypes_UML.png old mode 100644 new mode 100755 diff --git a/doc/source/UML/ObiDMS_UML.class.violet.html b/doc/source/UML/ObiDMS_UML.class.violet.html old mode 100644 new mode 100755 diff --git a/doc/source/containers.rst b/doc/source/containers.rst old mode 100644 new mode 100755 diff --git a/doc/source/data.rst b/doc/source/data.rst old mode 100644 new mode 100755 diff --git a/doc/source/elementary.rst b/doc/source/elementary.rst old mode 100644 new mode 100755 diff --git a/doc/source/guidelines.rst b/doc/source/guidelines.rst old mode 100644 new mode 100755 diff --git a/doc/source/images/history.png b/doc/source/images/history.png old mode 100644 new mode 100755 diff --git a/doc/source/images/version_control.png b/doc/source/images/version_control.png old mode 100644 new mode 100755 diff --git a/doc/source/index.rst b/doc/source/index.rst old mode 100644 new mode 100755 diff --git a/doc/source/specialvalues.rst b/doc/source/specialvalues.rst old mode 100644 new mode 100755 diff --git a/doc/source/types.rst b/doc/source/types.rst old mode 100644 new mode 100755 diff --git a/python/obi.py b/python/obi.py old mode 100644 new mode 100755 diff --git a/python/obitools3/__init__.py b/python/obitools3/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/__init__.pyc b/python/obitools3/__init__.pyc old mode 100644 new mode 100755 diff --git a/python/obitools3/align/__init__.py b/python/obitools3/align/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_assemble.pxd b/python/obitools3/align/_assemble.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_assemble.pyx b/python/obitools3/align/_assemble.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_dynamic.pxd b/python/obitools3/align/_dynamic.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_dynamic.pyx b/python/obitools3/align/_dynamic.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_nws.pxd b/python/obitools3/align/_nws.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_nws.pyx b/python/obitools3/align/_nws.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_qsassemble.pyx b/python/obitools3/align/_qsassemble.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_qsrassemble.pyx b/python/obitools3/align/_qsrassemble.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_rassemble.pxd b/python/obitools3/align/_rassemble.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_rassemble.pyx b/python/obitools3/align/_rassemble.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/_solexapairend.pyx b/python/obitools3/align/_solexapairend.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/align/solexapairend.py b/python/obitools3/align/solexapairend.py old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/__init__.py b/python/obitools3/apps/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/arguments.pxd b/python/obitools3/apps/arguments.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/arguments.pyx b/python/obitools3/apps/arguments.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/command.pxd b/python/obitools3/apps/command.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/command.pyx b/python/obitools3/apps/command.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/config.pxd b/python/obitools3/apps/config.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/config.pyx b/python/obitools3/apps/config.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/logging.pxd b/python/obitools3/apps/logging.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/logging.pyx b/python/obitools3/apps/logging.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/optiongroups/__init__.py b/python/obitools3/apps/optiongroups/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/progress.pxd b/python/obitools3/apps/progress.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/progress.pyx b/python/obitools3/apps/progress.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/temp.pxd b/python/obitools3/apps/temp.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/apps/temp.pyx b/python/obitools3/apps/temp.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/__init__.py b/python/obitools3/commands/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/alignpairedend.pyx b/python/obitools3/commands/alignpairedend.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/annotate.pyx b/python/obitools3/commands/annotate.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/count.pyx b/python/obitools3/commands/count.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/ecopcr.pyx b/python/obitools3/commands/ecopcr.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/export.pyx b/python/obitools3/commands/export.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/grep.pyx b/python/obitools3/commands/grep.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/history.pyx b/python/obitools3/commands/history.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/less.pyx b/python/obitools3/commands/less.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/ls.pyx b/python/obitools3/commands/ls.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/ngsfilter.pyx b/python/obitools3/commands/ngsfilter.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/sort.pyx b/python/obitools3/commands/sort.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/stats.pyx b/python/obitools3/commands/stats.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/test.pyx b/python/obitools3/commands/test.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/uniq.pxd b/python/obitools3/commands/uniq.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/__init__.py b/python/obitools3/dms/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/__init__.py b/python/obitools3/dms/capi/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obialign.pxd b/python/obitools3/dms/capi/obialign.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obiclean.pxd b/python/obitools3/dms/capi/obiclean.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obidms.pxd b/python/obitools3/dms/capi/obidms.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obidmscolumn.pxd b/python/obitools3/dms/capi/obidmscolumn.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obiecopcr.pxd b/python/obitools3/dms/capi/obiecopcr.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obierrno.pxd b/python/obitools3/dms/capi/obierrno.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obitaxonomy.pxd b/python/obitools3/dms/capi/obitaxonomy.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obitypes.pxd b/python/obitools3/dms/capi/obitypes.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obiutils.pxd b/python/obitools3/dms/capi/obiutils.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/capi/obiview.pxd b/python/obitools3/dms/capi/obiview.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/__init__.py b/python/obitools3/dms/column/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/column.pxd b/python/obitools3/dms/column/column.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/column.pyx b/python/obitools3/dms/column/column.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/column_idx.pxd b/python/obitools3/dms/column/column_idx.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/column_idx.pyx b/python/obitools3/dms/column/column_idx.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/__init__.py b/python/obitools3/dms/column/typed_column/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/bool.pxd b/python/obitools3/dms/column/typed_column/bool.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/bool.pyx b/python/obitools3/dms/column/typed_column/bool.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/char.pxd b/python/obitools3/dms/column/typed_column/char.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/char.pyx b/python/obitools3/dms/column/typed_column/char.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/float.pxd b/python/obitools3/dms/column/typed_column/float.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/float.pyx b/python/obitools3/dms/column/typed_column/float.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/int.pxd b/python/obitools3/dms/column/typed_column/int.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/int.pyx b/python/obitools3/dms/column/typed_column/int.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/qual.pxd b/python/obitools3/dms/column/typed_column/qual.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/qual.pyx b/python/obitools3/dms/column/typed_column/qual.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/seq.pxd b/python/obitools3/dms/column/typed_column/seq.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/seq.pyx b/python/obitools3/dms/column/typed_column/seq.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/str.pxd b/python/obitools3/dms/column/typed_column/str.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/column/typed_column/str.pyx b/python/obitools3/dms/column/typed_column/str.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/dms.cfiles b/python/obitools3/dms/dms.cfiles old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/dms.pxd b/python/obitools3/dms/dms.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/dms.pyx b/python/obitools3/dms/dms.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/obiseq.pxd b/python/obitools3/dms/obiseq.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/obiseq.pyx b/python/obitools3/dms/obiseq.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/object.pxd b/python/obitools3/dms/object.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/object.pyx b/python/obitools3/dms/object.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/taxo/__init__.py b/python/obitools3/dms/taxo/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/taxo/taxo.pxd b/python/obitools3/dms/taxo/taxo.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/taxo/taxo.pyx b/python/obitools3/dms/taxo/taxo.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/view/__init__.py b/python/obitools3/dms/view/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/view/typed_view/__init__.py b/python/obitools3/dms/view/typed_view/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/dms/view/view.pxd b/python/obitools3/dms/view/view.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/files/__init__.py b/python/obitools3/files/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/files/linebuffer.pxd b/python/obitools3/files/linebuffer.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/files/linebuffer.pyx b/python/obitools3/files/linebuffer.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/files/uncompress.pxd b/python/obitools3/files/uncompress.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/files/uncompress.pyx b/python/obitools3/files/uncompress.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/files/universalopener.pxd b/python/obitools3/files/universalopener.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/files/universalopener.pyx b/python/obitools3/files/universalopener.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/format/__init__.py b/python/obitools3/format/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/format/fasta.pxd b/python/obitools3/format/fasta.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/format/fasta.pyx b/python/obitools3/format/fasta.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/format/fastq.pxd b/python/obitools3/format/fastq.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/format/fastq.pyx b/python/obitools3/format/fastq.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/format/header.pxd b/python/obitools3/format/header.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/format/header.pyx b/python/obitools3/format/header.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/__init__.py b/python/obitools3/parsers/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/embl.pxd b/python/obitools3/parsers/embl.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/embl_genbank_features.pxd b/python/obitools3/parsers/embl_genbank_features.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/embl_genbank_features.pyx b/python/obitools3/parsers/embl_genbank_features.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/fasta.pxd b/python/obitools3/parsers/fasta.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/fasta.pyx b/python/obitools3/parsers/fasta.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/fastq.pxd b/python/obitools3/parsers/fastq.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/fastq.pyx b/python/obitools3/parsers/fastq.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/header.pxd b/python/obitools3/parsers/header.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/header.pyx b/python/obitools3/parsers/header.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/ngsfilter.pxd b/python/obitools3/parsers/ngsfilter.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/ngsfilter.pyx b/python/obitools3/parsers/ngsfilter.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/tab.pxd b/python/obitools3/parsers/tab.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/tab.pyx b/python/obitools3/parsers/tab.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/universal.pxd b/python/obitools3/parsers/universal.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/parsers/universal.pyx b/python/obitools3/parsers/universal.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/uri/__init__.py b/python/obitools3/uri/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/uri/decode.pxd b/python/obitools3/uri/decode.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/utils.cfiles b/python/obitools3/utils.cfiles old mode 100644 new mode 100755 diff --git a/python/obitools3/utils.pxd b/python/obitools3/utils.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/utils.pyx b/python/obitools3/utils.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/version.py b/python/obitools3/version.py old mode 100644 new mode 100755 diff --git a/python/obitools3/version.pyc b/python/obitools3/version.pyc old mode 100644 new mode 100755 diff --git a/python/obitools3/writers/__init__.py b/python/obitools3/writers/__init__.py old mode 100644 new mode 100755 diff --git a/python/obitools3/writers/fasta.pxd b/python/obitools3/writers/fasta.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/writers/fasta.pyx b/python/obitools3/writers/fasta.pyx old mode 100644 new mode 100755 diff --git a/python/obitools3/writers/fastq.pxd b/python/obitools3/writers/fastq.pxd old mode 100644 new mode 100755 diff --git a/python/obitools3/writers/fastq.pyx b/python/obitools3/writers/fastq.pyx old mode 100644 new mode 100755 diff --git a/requirements.txt b/requirements.txt old mode 100644 new mode 100755 diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 diff --git a/src/_sse.h b/src/_sse.h old mode 100644 new mode 100755 diff --git a/src/array_indexer.c b/src/array_indexer.c old mode 100644 new mode 100755 diff --git a/src/array_indexer.h b/src/array_indexer.h old mode 100644 new mode 100755 diff --git a/src/char_str_indexer.c b/src/char_str_indexer.c old mode 100644 new mode 100755 diff --git a/src/char_str_indexer.h b/src/char_str_indexer.h old mode 100644 new mode 100755 diff --git a/src/crc64.c b/src/crc64.c old mode 100644 new mode 100755 diff --git a/src/crc64.h b/src/crc64.h old mode 100644 new mode 100755 diff --git a/src/dna_seq_indexer.c b/src/dna_seq_indexer.c old mode 100644 new mode 100755 diff --git a/src/dna_seq_indexer.h b/src/dna_seq_indexer.h old mode 100644 new mode 100755 diff --git a/src/encode.c b/src/encode.c old mode 100644 new mode 100755 diff --git a/src/encode.h b/src/encode.h old mode 100644 new mode 100755 diff --git a/src/hashtable.c b/src/hashtable.c old mode 100644 new mode 100755 diff --git a/src/hashtable.h b/src/hashtable.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/ecoError.c b/src/libecoPCR/ecoError.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/ecoMalloc.c b/src/libecoPCR/ecoMalloc.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/ecoPCR.h b/src/libecoPCR/ecoPCR.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/ecoapat.c b/src/libecoPCR/ecoapat.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/ecodna.c b/src/libecoPCR/ecodna.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/CODES/dft_code.h b/src/libecoPCR/libapat/CODES/dft_code.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/CODES/dna_code.h b/src/libecoPCR/libapat/CODES/dna_code.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/CODES/prot_code.h b/src/libecoPCR/libapat/CODES/prot_code.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/Gmach.h b/src/libecoPCR/libapat/Gmach.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/Gtypes.h b/src/libecoPCR/libapat/Gtypes.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/apat.h b/src/libecoPCR/libapat/apat.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/apat_parse.c b/src/libecoPCR/libapat/apat_parse.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/apat_search.c b/src/libecoPCR/libapat/apat_search.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/libstki.c b/src/libecoPCR/libapat/libstki.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libapat/libstki.h b/src/libecoPCR/libapat/libstki.h old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libthermo/nnparams.c b/src/libecoPCR/libthermo/nnparams.c old mode 100644 new mode 100755 diff --git a/src/libecoPCR/libthermo/nnparams.h b/src/libecoPCR/libthermo/nnparams.h old mode 100644 new mode 100755 diff --git a/src/libjson/cJSON.c b/src/libjson/cJSON.c old mode 100644 new mode 100755 diff --git a/src/libjson/cJSON.h b/src/libjson/cJSON.h old mode 100644 new mode 100755 diff --git a/src/libjson/json_utils.c b/src/libjson/json_utils.c old mode 100644 new mode 100755 diff --git a/src/libjson/json_utils.h b/src/libjson/json_utils.h old mode 100644 new mode 100755 diff --git a/src/linked_list.c b/src/linked_list.c old mode 100644 new mode 100755 diff --git a/src/linked_list.h b/src/linked_list.h old mode 100644 new mode 100755 diff --git a/src/obi_align.c b/src/obi_align.c old mode 100644 new mode 100755 diff --git a/src/obi_align.h b/src/obi_align.h old mode 100644 new mode 100755 diff --git a/src/obi_clean.h b/src/obi_clean.h old mode 100644 new mode 100755 diff --git a/src/obi_ecopcr.c b/src/obi_ecopcr.c old mode 100644 new mode 100755 diff --git a/src/obi_ecopcr.h b/src/obi_ecopcr.h old mode 100644 new mode 100755 diff --git a/src/obiavl.c b/src/obiavl.c old mode 100644 new mode 100755 diff --git a/src/obiavl.h b/src/obiavl.h old mode 100644 new mode 100755 diff --git a/src/obiblob.c b/src/obiblob.c old mode 100644 new mode 100755 diff --git a/src/obiblob.h b/src/obiblob.h old mode 100644 new mode 100755 diff --git a/src/obiblob_indexer.c b/src/obiblob_indexer.c old mode 100644 new mode 100755 diff --git a/src/obiblob_indexer.h b/src/obiblob_indexer.h old mode 100644 new mode 100755 diff --git a/src/obidebug.h b/src/obidebug.h old mode 100644 new mode 100755 diff --git a/src/obidms.c b/src/obidms.c old mode 100644 new mode 100755 diff --git a/src/obidms.h b/src/obidms.h old mode 100644 new mode 100755 diff --git a/src/obidms_taxonomy.c b/src/obidms_taxonomy.c old mode 100644 new mode 100755 diff --git a/src/obidms_taxonomy.h b/src/obidms_taxonomy.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn.c b/src/obidmscolumn.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn.h b/src/obidmscolumn.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_array.c b/src/obidmscolumn_array.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_array.h b/src/obidmscolumn_array.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_blob.c b/src/obidmscolumn_blob.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_blob.h b/src/obidmscolumn_blob.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_bool.c b/src/obidmscolumn_bool.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_bool.h b/src/obidmscolumn_bool.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_char.c b/src/obidmscolumn_char.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_char.h b/src/obidmscolumn_char.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_float.c b/src/obidmscolumn_float.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_float.h b/src/obidmscolumn_float.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_idx.c b/src/obidmscolumn_idx.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_idx.h b/src/obidmscolumn_idx.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_int.c b/src/obidmscolumn_int.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_int.h b/src/obidmscolumn_int.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_qual.c b/src/obidmscolumn_qual.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_qual.h b/src/obidmscolumn_qual.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_seq.c b/src/obidmscolumn_seq.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_seq.h b/src/obidmscolumn_seq.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_str.c b/src/obidmscolumn_str.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumn_str.h b/src/obidmscolumn_str.h old mode 100644 new mode 100755 diff --git a/src/obidmscolumndir.c b/src/obidmscolumndir.c old mode 100644 new mode 100755 diff --git a/src/obidmscolumndir.h b/src/obidmscolumndir.h old mode 100644 new mode 100755 diff --git a/src/obierrno.c b/src/obierrno.c old mode 100644 new mode 100755 diff --git a/src/obierrno.h b/src/obierrno.h old mode 100644 new mode 100755 diff --git a/src/obilittlebigman.c b/src/obilittlebigman.c old mode 100644 new mode 100755 diff --git a/src/obilittlebigman.h b/src/obilittlebigman.h old mode 100644 new mode 100755 diff --git a/src/obitypes.c b/src/obitypes.c old mode 100644 new mode 100755 diff --git a/src/obitypes.h b/src/obitypes.h old mode 100644 new mode 100755 diff --git a/src/obiview.c b/src/obiview.c old mode 100644 new mode 100755 diff --git a/src/obiview.h b/src/obiview.h old mode 100644 new mode 100755 diff --git a/src/sse_banded_LCS_alignment.c b/src/sse_banded_LCS_alignment.c old mode 100644 new mode 100755 diff --git a/src/sse_banded_LCS_alignment.h b/src/sse_banded_LCS_alignment.h old mode 100644 new mode 100755 diff --git a/src/uint8_indexer.c b/src/uint8_indexer.c old mode 100644 new mode 100755 diff --git a/src/uint8_indexer.h b/src/uint8_indexer.h old mode 100644 new mode 100755 diff --git a/src/upperband.c b/src/upperband.c old mode 100644 new mode 100755 diff --git a/src/upperband.h b/src/upperband.h old mode 100644 new mode 100755 diff --git a/src/utils.c b/src/utils.c old mode 100644 new mode 100755 diff --git a/src/utils.h b/src/utils.h old mode 100644 new mode 100755