Initial commit

README.md

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+# Callstate
+A tool that generates similar results as CallableLoci in GATK3 but runs much faster.
+
+## Algorithm
+This tool uses similar depth calculating algorithm in Mosdepth to calculate the raw depth, qc depth and low_mapq depth and then uses the same algorithm in CallableLoci tool in GATK3 to determine the following callable states:
+
+ - REF_N
+ - NO_COVERAGE
+ - LOW_COVERAGE
+ - POOR_MAPPING_QUALITY
+ - EXCESSIVE_COVERAGE
+ - CALLABLE
+
+For each region in the output file, besides the location of region, Callstate also outputs the mean raw depth, mean QC depth, and the mean Low MAPQ depth 
+
+## Usage
+```
+callstate 0.0.1
+
+  Usage: callstate [options] <BED> <BAM>
+
+Arguments:
+
+  <BAM>  the alignment file for which to calculate callable states
+  <BED>  The BED file that contains regions.
+
+Common Options:
+
+  -t --threads <threads>                 Number of BAM decompression threads [default: 4]
+  -o --output <output>                   The output BED file.
+  -mbq --min-base-qual <mbq>             The minimum base quality for a base to contribute to QC depth [default: 10]
+  -mmq --min-mapq <mmq>                  The minimum mapping quality of reads to count as QC depth [default: 10]
+  -mdp --min-depth <mdp>                 The minimum QC read depth before a read is considered callable [default: 20]
+  -mlmq --max-low-mapq <mlmq>            The maximum value of MAPQ before a read is considered as problematic mapped read. [default: 1]
+  -mxdp --max-depth <mxdp>               The maximum read depth before a locus is considered high coverage [default: -1]
+  -mdflmq --min-depth-low-mapq <mdflmq>  Minimum read depth before a locus is considered candidate for poorly mapped [default: 10]
+  -frlmq --low-mapq-frac <frlmq>         If the fraction of low mapping reads exceeds this value, the site is considered poorly mapped [default: 0.5]
+
+Other options:
+
+  -F --flag <FLAG >                      exclude reads with any of the bits in FLAG set [default: 1796]
+  -h --help                              show help
+```
+
+## Examples
+To run with default values for all parameters:
+```
+callstate -o <output.bed> <capture.bed> <bam/final.bam>
+```
+
+## Sample output
+```
+#chrom  start   end     call_state      raw_depth       qc_depth        low_mapq_depth
+22      17565780        17566404        CALLABLE        309.22  305.61  0.00
+22      17577753        17577787        LOW_COVERAGE    10.41   9.76    0.00
+22      17577787        17577789        POOR_MAPPING_QUALITY    161.78  31.23   129.76
+22      17577789        17577790        LOW_COVERAGE    20.00   19.00   0.00
+22      17577790        17578173        CALLABLE        120.22  119.55  0.00
+```

callstate.nimble

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+# Package
+
+version       = "0.0.1"
+author        = "Luobin Yang"
+description   = "GATK3 CallableLoci Replacement"
+license       = "MIT"
+
+# Dependencies
+
+requires "hts >= 0.2.23", "nim >= 1.0.0", "docopt >= 0.6.8"
+
+srcDir = "src"
+
+bin = @["callstate"]
+skipDirs = @["tests"]
+
+
+task test, "run the tests":
+  exec "nim c --lineDir:on --debuginfo -r tests/test_state"