update README.md

README.md

@@ -1,13 +1,13 @@
-#### Usage
+### Choppy APP Usage
 $ open-choppy-env
 $ choppy install YaqingLiu/bamdst
 $ choppy batch YaqingLiu/bamdst-latest samples.csv -p project_name
 
-#### samples.csv
+### samples.csv
 sample_id,sample,bam,bed
 
 
-# bamdst -- a BAM Depth Stat Tool
+### bamdst -- a BAM Depth Stat Tool
 
 Bamdst is a lightweight tool to stat the depth coverage of  target regions of bam file(s).
 
@@ -15,7 +15,7 @@ Bam file(s) should be properly sorted, and the probe file (bed file) and the out
 
 must be specified in the first place.
 
-## USAGE
+#### USAGE
 
 Normal:
 
@@ -25,7 +25,7 @@ Pipeline mode:
 
     samtools view in1.bam -u | bamdst -p x.bed -o ./ -
 
-## PARAMETERS
+#### PARAMETERS
 
 -o / --outdir [dir]
 
@@ -35,55 +35,17 @@ set the output dir [mandatory]
 
 the probe or captured target region file, these regions will be merged first [mandatory]
 
-## OPTIONAL PARAMETERS
-
--f / --flank [num]
-
-if you want calculate the coverage of flank region, set this value, default is 200
-
---maxdepth [num]
-
-for some projects, the depths of sepcial region are very high, if you don't want show
-
-these unnormal depths in cumulation distrbution file, set the cutoff value to filter them.
-
-default is 0 (no filter).
-
---cutoffdepth [num]
-
-for some projects, people care about the coverage of specified depth, like 10000x etc.
-
-bamdst just calculate the coverage of 0x, 4x, 10x, 30x, 100x, so you can set this value
-
-to show the specified coverage in the coverage.report file. Default is 0.
-
---isize [num]
-
-for bad mapped paired reads, the inferred insert size is very huge. So set a cutoff
-
-value for reasonal visual purpose. Default is 2000.
-
---uncover [num]
-
-set this cutoff value for calculate the bad covered region. Default is <5.
-
---use_rmdup (an invalid parament since v1.0.0 )
-
-Use rmdup depth instead of cover depth to calculate the coverage of target regions and
-
-so on.
-
-## OUTPUT FILES
+#### OUTPUT FILES
 
 Seven files will be created in the output direction. There are:
 
 -**coverage.report**
 
--**cumu.plot**
+-**depth_distribution.plot**
 
--**insert.plot**
+-**insertsize.plot**
 
--**chromosome.report**
+-**chromosomes.report**
 
 -**region.tsv.gz**
 
@@ -91,7 +53,7 @@ Seven files will be created in the output direction. There are:
 
 -**uncover.bed**
 
-## DETAILS of each file
+#### DETAILS of each file
 
 **coverage.report**
 
@@ -101,10 +63,10 @@ flank region, and reads stat information of the input file(s).
 
 Here is the full details of each entry.
 
-     [Total] Raw Reads (All reads) // All reads in the bam file(s).
-     [Total] QC Fail reads // Reads number failed QC, this flag is marked by other software,like bwa. See flag in the bam structure.
-     [Total] Raw Data(Mb) // Total reads data in the bam file(s).
-     [Total] Paired Reads // Paired reads numbers.
+    [Total] Raw Reads (All reads) // All reads in the bam file(s).
+    [Total] QC Fail reads // Reads number failed QC, this flag is marked by other software,like bwa. See flag in the bam structure.
+    [Total] Raw Data(Mb) // Total reads data in the bam file(s).
+    [Total] Paired Reads // Paired reads numbers.
     [Total] Mapped Reads // Mapped reads numbers.
     [Total] Fraction of Mapped Reads // Ratio of mapped reads against raw reads.
     [Total] Mapped Data(Mb) // Mapped data in the bam file(s).
@@ -165,15 +127,15 @@ Here is the full details of each entry.
     [flank] Coverage (>=30x) // Ratio of flank bases with depth greater than or equal to 30x.
 
 
-**cumu.plot**
+**depth_distribution.plot**
 
 Depth distrbution for plot.
 
-**insert.plot**
+**insertsize.plot**
 
 Inferred insert size distribution for plot.
 
-**chromosome.report**
+**chromosomes.report**
 
 Depth and coverage information of each chromosome.
 
@@ -217,6 +179,6 @@ input bam file(s) against the probe file. Set the cutoff value of
 
 uncover by parameter "--uncover"
 
-# Known bugs
+#### Known bugs
 
 For a large region, like whole genome region, bamdst may go crash with a segmental fault. I have noticed issues like this, and this bug can be tolerated by split a large region into several small pieces. However, this bug may not be fixed until next major update.