Epic alignment changes

.gitignore

@@ -22,6 +22,7 @@ test.aligned.stats
 test.allelotype.stats
 test.post
 data/strinfo.hg19_1to6.tab
+test_data/*
 
 Makefile.in
 aclocal.m4

Makefile.am

@@ -8,23 +8,12 @@
 # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the
 # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
-DATA_FILES = \
-	data/lobstr.allelepriors.hg19.min50.tab \
-	data/trf.ucsc.hg19.filtered.bed \
-	data/trf.ucsc.hg18.filtered.bed \
-	data/strinfo.hg18.tab \
-	data/strinfo.hg19.tab \
-	data/vcf_positions_to_exclude_hg18.tab \
-	data/vcf_positions_to_exclude_hg19.tab
-
-
 EXTRA_DIST = reconf configure \
 	config/git-version-gen \
 	config/gen-coverage-report.sh \
 	config/rebuild-coverage.sh \
 	lobSTR.rb \
-	$(top_srcdir)/.version \
-	$(DATA_FILES)
+	$(top_srcdir)/.version
 
 SUBDIRS = m4 src scripts models tests
 ACLOCAL_AMFLAGS = -I m4

README

@@ -1 +1,5 @@
-For full documentation, see the lobSTR website: http://lobstr.teamerlich.org/
+For full documentation, see the lobSTR website: http://lobstr.teamerlich.org/
+
+NOTE: the git repository is currently under construction as we are working on lobSTR v3. This release contains major changes to our STR calling algorithm ans is in *alpha* mode. Use at your own risk. Stable lobSTR releases can be found on the lobSTR website.
+
+lobSTR v3 requires a new index and will not work with previous indices. The new hg19 index can be found here: http://files.teamerlich.org/lobstr/v3/ref/lobSTR_v3_hg19_resource_bundle.tar.gz.

configure.ac

@@ -27,7 +27,6 @@ AC_PROG_INSTALL
 PKG_CHECK_MODULES([GSL],[gsl])
 
 
-PKG_CHECK_MODULES([FFTW], [fftw3])
 AX_PTHREAD([],[
    AC_MSG_ERROR([Pthread support is required for LobSTR])
 ])