Changeset 3317

Timestamp:

Sep 19, 2014, 7:41:50 AM (9 years ago)

Author:

Peter

Message:

refs #806 add test for Pileup class

Location:

trunk

Files:

• test/Makefile.am (modified) (2 diffs)
• test/pileup.cc (added)
• yat/omic/Makefile.am (modified) (1 diff)
• yat/omic/Pileup.h (modified) (6 diffs)

trunk/test/Makefile.am

@@ -71 +71 @@
   test/ostream_iterator.test \
   test/pca.test \
+  test/pileup.test \
   test/queue.test test/queue2.test \
   test/range.test test/regression.test test/rnd.test \
@@ -136 +137 @@
 
 # dependencies for lazycheck
+test/bam.log: test/data/foo.sorted.bam
+test/bam_header.log: test/data/foo.sorted.bam
+test/bam_header2.log: test/data/foo.sorted.bam
+test/bam_iterator.log: test/data/foo.sorted.bam
+test/bam_pair_analyse.log: test/data/foo.sorted.bam
+test/bam_pair_iterator.log: test/data/foo.sorted.bam
+test/bam_read_filter.log: test/data/foo.sorted.bam
+test/bam_region_iterator.log: test/data/foo.sorted.bam
 test/cmd_test.log: test/help.test $(shell_test_deps)
 test/help_test.log: test/help.test $(shell_test_deps)
+test/pileup.log: test/data/foo.sorted.bam
 test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
 test/yat_config_test.log: build_support/yat-config \

trunk/yat/omic/Makefile.am

@@ -50 +50 @@
 nobase_include_HEADERS += $(srcdir)/yat/omic/GFF2.h
 nobase_include_HEADERS += $(srcdir)/yat/omic/GFF3.h
+nobase_include_HEADERS += $(srcdir)/yat/omic/Pileup.h

trunk/yat/omic/Pileup.h

@@ -33 +33 @@
 namespace omic {
 
+  /**
+     \since new in yat 0.13
+   */
   template<typename Iterator>
   class Pileup
@@ -55 +58 @@
       const yat::omic::BamRead& bam(void) const { return bam_; }
 
+      /**
+         \return cigar element at current position
+       */
       uint32_t cigar(void) const
       {
@@ -102 +108 @@
       }
 
+      /**
+         \return index of base at this position
+       */
       size_t qpos(void) const { return qpos_; }
     private:
@@ -118 +127 @@
     };
 
-    // FIXME change to a filter iterator that ignores end_of_sequence entries
+    /**
+       \brief Const iterator that can be used to iterate over reads at
+       current position
+     */
     typedef typename std::deque<Entry>::const_iterator const_iterator;
 
@@ -147 +159 @@
 
     /**
+       \brief step to next position with coverage
      */
     void increment(void);
@@ -177 +190 @@
 
 
+  /**
+     \relates Pileup
+
+     \since new in yat 0.13
+   */
   template<typename Iterator>
   Pileup<Iterator> make_pileup(Iterator first, Iterator last)