Adding RNAseq feature

ncbi · Jun 20, 2019 · 4130f05 · 4130f05
1 parent c0bc2c1
commit 4130f05
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Showing 12 changed files with 563 additions and 52 deletions.
diff --git a/includes/BAMcoverage.h b/includes/BAMcoverage.h
@@ -35,8 +35,11 @@ extern "C" {
     char *BEDentryChr(char *input);
     void SubtractBlacklistedBEDS(char *filename, CHROMOSOMES *head, BAMFILES *bhead, int paired_end);
     int *CalculateCoverage(samFile *fp_in, hts_itr_t *iter, bam1_t *aln, int chrsize, char *chrname, CMDINPUT *cmd, BAMFILES *bamcurr);
+    void GetGenomeCoverageRNA(CMDINPUT *cmd, CHROMOSOMES *head, char *outfile);
     void *GetGenomeCoveragemultithread(void * voidA);
     void MultiGenomeCoverage(CMDINPUT *cmd, CHROMOSOMES *chr);
+    void *GetGenomeBaseCoveragemultithread(void * voidA);
+    void MultiGenomeBaseCoverage(CMDINPUT *cmd, CHROMOSOMES *chr);
     void *ScaleBinsmultithread(void * voidA);
     void MultiGenomeScaler(CMDINPUT *cmd, CHROMOSOMES *chr);
     void *SmoothBinsmultithread(void * voidA);

diff --git a/includes/Definitions.h b/includes/Definitions.h
@@ -138,11 +138,15 @@ extern "C" {
         int argc;
         int genome_coverage;
         int strandsplit;
+        char *custom_scale;
 
         char *normtype;
         char *scale;
         char *operation;
 
+        int filtDiffChr;
+        int filtInsSize;
+
         int binSize;
         int binSizeChange;
         int smoothBin;

diff --git a/includes/Inputs.h b/includes/Inputs.h
@@ -20,12 +20,16 @@
 #define INPUTS_BASE "base"
 #define INPUTS_GENOME "genome"
 #define INPUTS_SCALED "scaled"
+#define INPUTS_CUSTOM "custom"
 #define INPUTS_SCALE "scale"
 #define INPUTS_UNSCALED "unscaled"
 #define INPUTS_LOG2 "log2"
 #define INPUTS_RFD "rfd"
 #define INPUTS_END "endseq"
 #define INPUTS_ENDR "endseqr"
+#define INPUTS_RNA "rna"
+#define INPUTS_STRRNA "strandrna"
+#define INPUTS_RSTRRNA "strandrnaR"
 #define INPUTS_REP "reptime"
 #define INPUTS_RATIO "ratio"
 #define INPUTS_SUBSTRACT "subtract"
@@ -41,6 +45,7 @@
 extern "C" {
 #endif
     CMDINPUT *CreateCMDinput(void);
+    int ParseCustomScaling(CMDINPUT *cmd, char *scales);
     void PrintScaleMessage(char *pname);
     CMDINPUT *ScaleParser(int argc, char **argv);
     void PrintMultiCovMessage(char *pname);

diff --git a/includes/Writer.h b/includes/Writer.h
@@ -20,6 +20,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
+    char *returnRNAfilename(CMDINPUT *cmd);
     void PrintScaledBigWig(CMDINPUT *cmd, BAMFILES *curr, char *sfile);
 #ifdef __cplusplus
 }

diff --git a/includes/main.h b/includes/main.h
@@ -20,6 +20,7 @@ extern "C" {
 #endif
     void FreeAllocatedData(void);
     void ComputeCoverageChIPpeak(CMDINPUT *cmd);
+    void NormalizeBAMSrna(CMDINPUT *cmd);
     void NormalizeBAMS(CMDINPUT *cmd);
     void PrintUsage(char *pname);
     int main();

diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml
@@ -6,8 +6,6 @@
     </data>
     <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
     <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
-        <group>
-            <file>file:/Users/veraalva/Work/Developer/C/BAMscale/Dockerfile</file>
-        </group>
+        <group/>
     </open-files>
 </project-private>