inc R datautils version to 1.9; better counting

chipseq_workflow/chipseq_utils.sh

-#source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
+#source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
 
 
 ## configure paths
@@ -14,8 +14,8 @@ export PYTHONPATH=/home/brandl/bin/macs2/lib/python2.7/site-packages:$PYTHONPATH
 cs_bowtie_qc(){
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/ggplot_commons.R")
 
 ########################################################################################################################
 #> # Bowtie2 Mapping Summary
@@ -132,16 +132,26 @@ if [ $# -ne 2 ]; then
 fi
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/core_commons.R")
 
 bamFile=commandArgs(T)[1]
 chromInfoFile=commandArgs(T)[2]
 
-#bamFile="/projects/bioinfo/holger/projects/khan_chipseq_h1/alignments_mmfilt/H1M_Dome_mmf.bam";
-#bedFile="danRer7.chromInfo"
+#bamFile="/projects/bioinfo/holger/projects/krause_chipseq/alignments_mmfilt/H3HA_Dome_mmf.bam";
+#chromInfoFile="danRer7.chromInfo"
 
 chrOrderBam <- readLines(pipe(paste("samtools view -H ", bamFile, " | cut -f2 | grep -F SN"))) %>% str_replace(fixed("SN:"), "")
+
+chromInfo <- read.delim(chromInfoFile) %>% mutate(chrom=str_replace(chrom, "chr", ""))
+
+#data.frame(chrom=chrOrderBam) %>%
+#    left_join(chromInfo) %>%
+#    ## make sure to always keep all chromsomes of the bam no matter if they are present in the chromInfo.
+#    mutate(size=ifelse(is.na(size), -1, size)) %>%
+#    write.delim(stdout(), header=F, quote=F)
+
 read.delim(chromInfoFile) %>%
+    mutate(chrom=str_replace(chrom, "chrM", "MT")) %>%
     mutate(chrom=str_replace(chrom, "chr", "")) %>%
     mutate(chrom=factor(as.character(chrom), levels=chrOrderBam)) %>% arrange(chrom) %>%
     filter(!is.na(chrom)) %>%
@@ -158,7 +168,7 @@ if [ $# -ne 2 ]; then
 fi
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/core_commons.R")
 
 bamFile=commandArgs(T)[1]
 bedFile=commandArgs(T)[2]