Set avg minimal coverage to call a fragment as deleted at 3.0... eith…

…er fit if successful or straight average

ChangeLog

@@ -1,7 +1,7 @@
-Version 0.30.3
-   * Fixed critical error that could give negative positions when a reference sequence fragment
-     was called as deleted.
-   * Fixed  rare case where fitting coverage distribution could lead to fatal error.
+Version 0.31.0
+   * Fixed critical error that could give negative positions for mutations when a reference sequence 
+     fragment was called as deleted.
+   * Fixed several cases where fitting coverage distribution could fail or lead to a fatal error.
 
 Version 0.30.2
    * Improved robustness of fitting coverage distribution and added fallbacks if fitting fails.

binarydist.sh

@@ -15,12 +15,13 @@ BINARYLOCALDIR=${BRESEQVERSIONSTRING}-${BINARYNAME}
 BINARYDIR=${PWD}/${BINARYLOCALDIR}
 rm -r ${BINARYDIR} ${BINARYDIR}.tgz
 
-echo "./configure CFLAGS=\"${ARCHFLAGS} ${CFLAGS}\" CXXFLAGS=\"${ARCHFLAGS} ${CXXFLAGS}\" LDFLAGS=\"${ARCHFLAGS} ${LDFLAGS}\" --prefix=\"${BINARYDIR}\"
-./configure CFLAGS="${ARCHFLAGS} ${CFLAGS}" CXXFLAGS="${ARCHFLAGS} ${CXXFLAGS}" LDFLAGS="${ARCHFLAGS} ${LDFLAGS}" --prefix="${BINARYDIR}"
+echo "${BINARYDIR}"
+echo "./configure --prefix=\"${BINARYDIR}\" CFLAGS=\"${ARCHFLAGS} ${CFLAGS}\" CXXFLAGS=\"${ARCHFLAGS} ${CXXFLAGS}\" LDFLAGS=\"${ARCHFLAGS} ${LDFLAGS}\""
+./configure --prefix="${BINARYDIR}" CFLAGS="${ARCHFLAGS} ${CFLAGS}" CXXFLAGS="${ARCHFLAGS} ${CXXFLAGS}" LDFLAGS="${ARCHFLAGS} ${LDFLAGS}"
 
 make clean
 make -j 6
-make test 
+make test
 make install
 
 #Documentation and information

configure.ac

@@ -19,7 +19,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.65])
-AC_INIT([breseq], [0.30.2b], [[email protected]], [breseq], [http://barricklab.org/breseq])
+AC_INIT([breseq], [0.31.0], [[email protected]], [breseq], [http://barricklab.org/breseq])
 AC_CONFIG_AUX_DIR(aux_build)
 AC_CONFIG_MACRO_DIR([aux_build/m4])
 AC_CONFIG_HEADERS([aux_build/config.h])

src/c/breseq/coverage_distribution.r

@@ -465,14 +465,20 @@ if (nb_fit_mu > 0) {
   cat("Mu estimate=", m," Size estimate =", size_estimate, "\n")
   deletion_propagation_coverage = qnbinom(deletion_propagation_pr_cutoff, size = size_estimate, mu = m)
   if (is.nan(deletion_propagation_coverage) || (deletion_propagation_coverage < 1)) {
-    cat("Double fallback to calculating as just 20% of the mean\n")
-    deletion_propagation_coverage = m * 0.2 
+    cat("Double fallback to calculating as just 10% of the mean\n")
+    deletion_propagation_coverage = m * 0.1
   }
 }
 
-#Call it as deleted if this number is also basically zero, implying very low coverage
+#Don't allow one read to indicate non-deleted regions
 if (deletion_propagation_coverage < 1) {
-    deletion_propagation_coverage = -1
+    deletion_propagation_coverage = 1
+}
+
+#This works fine with the negative values
+#If we have both low fit coverage and low straight average coverage then we're deleted...
+if ( (nb_fit_mu <= 3) && (m <= 3) ) {
+  deletion_propagation_coverage = -1
 }
 
 #print out statistics