bug fixes

bwa/Makefile

@@ -31,6 +31,8 @@ bwa:libbwa.a $(AOBJS) main.o
 
 ## JEREMIAH
 test: ; 
+dist: ;
+distdir: ;
 
 check: ;
 

htslib/Makefile

@@ -84,6 +84,9 @@ BUILT_TEST_PROGRAMS = \
 
 all: lib-static $(BUILT_PROGRAMS) ##$(BUILT_TEST_PROGRAMS)
 
+##JEREMIAH
+distdir: ;
+
 HTSPREFIX =
 include htslib_vars.mk
 

src/AlignedContig.cpp

@@ -754,7 +754,7 @@ bool AlignmentFragment::parseIndelBreak(BreakPoint &bp) {
   //bp.homology = "";
 
   int curr = 0;
-  int gcurrlen = -1;
+  int gcurrlen = 0; //-1;
 
   bp.gr1.pos1 = -1;
   bp.gr1.pos2 = -1;

src/BreakPoint.cpp

@@ -663,8 +663,8 @@ namespace SnowTools {
 
     int pos1 = gr1.pos1;
     bool isdel = insertion.length() == 0;
-    if (isdel) // del breaks are stored as last non-deleted base. CigarMap stores as THE deleted base
-      pos1++;
+    //if (isdel) // del breaks are stored as last non-deleted base. CigarMap stores as THE deleted base
+    //  pos1++;
     std::string st = std::to_string(gr1.chr) + "_" + std::to_string(pos1) + "_" + std::to_string(this->getSpan()) + (isdel ? "D" : "I");
     return st;
   }
@@ -771,21 +771,29 @@ namespace SnowTools {
     // set the allelic fraction
     double af_n = -1;
     double af_t = -1;
-    std::cerr << cname << " " << tcov_support << " " << ncov_support << std::endl;
+
     if (isindel && tcov > 0) 
       af_t = static_cast<double>(/*std::max(tsplit, tcigar)*/tcov_support) / static_cast<double>(tcov);
     if (isindel && ncov > 0) 
       af_n = static_cast<double>(/*std::max(nsplit, ncigar)*/ncov_support) / static_cast<double>(ncov);
 
+    std::string s_af_t = std::to_string(af_t);
+    if (s_af_t.length() > 4)
+      s_af_t = s_af_t.substr(0, 4);      
+    std::string s_af_n = std::to_string(af_n);
+    if (s_af_n.length() > 4)
+      s_af_n = s_af_n.substr(0, 4);
 
+    size_t rs_t = std::count(rs.begin(), rs.end(), 'r');
+
     if (isindel)
-      ss << ">>>> " << (insertion.size() ? "INSERTION" : "DELETION") <<  " of length " << getSpan() << " at " << gr1 << " contig " << cname 
+      ss << ">" << (insertion.size() ? "INS: " : "DEL: ") << getSpan() << " " << gr1 /*<< " "  << cname */
 	 << " T/N split: " << tsplit << "/" << nsplit << " T/N cigar: " 
-	 << tcigar << "/" << ncigar << " T/N AF " << af_t << "/" << af_n << " T/N Cov " << tcov << "/" << ncov << " DBSNP " << rs;
+	 << tcigar << "/" << ncigar << " T/N AF " << s_af_t << "/" << s_af_n << " T/N Cov " << tcov << "/" << ncov << " DBSNP: " << rs_t;
     else
-      ss << ">>>> STRUCTURAL VAR  at " << gr1.pointString() << " to " << gr2.pointString() << " SPAN " << getSpan() << " contig " << cname 
-	 << " T/N split: " << tsplit << "/" << nsplit << " T/N discordant: " 
-	 << dc.tcount << "/" << dc.ncount << " evidence " << evidence;
+      ss << "> SV: " << gr1.pointString() << " to " << gr2.pointString() << " SPAN " << getSpan() /*<< " "  << cname */
+	 << " T/N split: " << tsplit << "/" << nsplit << " T/N disc: " 
+	 << dc.tcount << "/" << dc.ncount << " " << evidence;
 
 
     return ss.str();

src/Makefile.in

@@ -20,7 +20,7 @@ VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
 pkglibdir = $(libdir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
-top_builddir = ..
+top_builddir = ../..
 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
 INSTALL = @INSTALL@
 install_sh_DATA = $(install_sh) -c -m 644
@@ -34,7 +34,7 @@ POST_INSTALL = :
 NORMAL_UNINSTALL = :
 PRE_UNINSTALL = :
 POST_UNINSTALL = :
-subdir = src
+subdir = SnowTools/src
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -204,9 +204,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  src/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  SnowTools/src/Makefile'; \
 	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign  src/Makefile
+	  $(AUTOMAKE) --foreign  SnowTools/src/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \

src/SnowTools/SnowToolsCommon.h

@@ -100,7 +100,7 @@ namespace SnowTools {
   static const int NONCENT_CHR [44] = {1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,
 				       11,11,12,12,13,14,15,16,16,17,17,18,18,19,19,20,20,21,21,22,23,23,24,24};
 
-  
+
 }
 
 #endif