Merge pull request #112 from wtsi-npg/devel

merge devel to master, preparation for release 10.27
wtsi-npg · Dec 14, 2016 · a2aa5dc · a2aa5dc
2 parents 36c9bba + 09114fd
commit a2aa5dc
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Showing 6 changed files with 1,184 additions and 2 deletions.
diff --git a/src/Makefile.am b/src/Makefile.am
@@ -1,2 +1,2 @@
 ACLOCAL_AMFLAGS = -I ac_stubs
-SUBDIRS = shared calibration_pu predictor_pu spatial_filter error_analysis
+SUBDIRS = shared calibration_pu predictor_pu spatial_filter error_analysis contamination
diff --git a/src/calibration_pu/calibration_pu.c b/src/calibration_pu/calibration_pu.c
@@ -1553,6 +1553,7 @@ SurvTable **makeSurvTable(Settings *s, samfile_t *fp_bam, int *bam_ntiles, size_
         if (BAM_FSECONDARY & bam->core.flag) continue;
         if (BAM_FSUPPLIMENTARY & bam->core.flag) continue;
         if (BAM_FPAIRED & bam->core.flag) {
+            if (BAM_FMUNMAP & bam->core.flag) continue;
             if (0 == (BAM_FPROPER_PAIR & bam->core.flag)) {
                 continue;
             }

diff --git a/src/configure.ac b/src/configure.ac
@@ -31,4 +31,4 @@ AX_LIB_IO_LIB(1.12.1,
 AX_LIB_ZLIB(,[have_zlib=yes], [AC_MSG_ERROR([Abort: no zlib. Please rerun configure using the --with-zlib=DIR option.])])
 AX_LIB_SAMTOOLS(0.1.3,[have_bam=yes],[AC_MSG_ERROR([Abort: no samtools. Please rerun configure using the ---with-samtools=DIR option.])])
 
-AC_OUTPUT(Makefile shared/Makefile calibration_pu/Makefile predictor_pu/Makefile spatial_filter/Makefile error_analysis/Makefile)
+AC_OUTPUT(Makefile shared/Makefile calibration_pu/Makefile predictor_pu/Makefile spatial_filter/Makefile error_analysis/Makefile contamination/Makefile)
diff --git a/src/contamination/Makefile.am b/src/contamination/Makefile.am
@@ -0,0 +1,11 @@
+bin_PROGRAMS = get_mixture get_thr_ploidy
+
+get_mixture_SOURCES = get_mixture.c
+
+get_mixture_LDADD = @IO_LIB_LDFLAGS@ @SAMTOOLS_LDFLAGS@ -L../shared -lhelper_funcs
+
+get_thr_ploidy_SOURCES = get_thr_ploidy.c
+
+get_thr_ploidy_LDADD = @IO_LIB_LDFLAGS@ @SAMTOOLS_LDFLAGS@ -L../shared -lhelper_funcs
+
+AM_CPPFLAGS = @IO_LIB_CFLAGS@ @SAMTOOLS_CFLAGS@ -I@top_srcdir@/shared