From 6fa3f6779e5f4f97df812d94b073ad353952f068 Mon Sep 17 00:00:00 2001
From: Daniel Cook <danielecook@gmail.com>
Date: Tue, 22 Oct 2019 12:03:21 +0100
Subject: [PATCH] fix fq_count var

---
 .gitignore       |  3 ++-
 sc.nim           | 16 +++++++++++++++-
 src/fq_count.nim | 12 +++++++-----
 tasks.todo       | 10 ++++++++++
 4 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index 90c9b95..1eb8faf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@ nimcache/
 tut
 ssshtest
 .Rhistory
-.python-version
\ No newline at end of file
+.python-version
+bam_set/
\ No newline at end of file
diff --git a/sc.nim b/sc.nim
index 569b14e..ec303d8 100644
--- a/sc.nim
+++ b/sc.nim
@@ -14,10 +14,12 @@ import sequtils
 import terminal
 import asyncfile
 import zip/gzipfiles
+
 import src/fq_meta
 import src/fq_count
 import src/fq_dedup
-#import src/index_swap
+import src/vcf2tsv
+
 import src/utils/helpers
 from constants import ANN_header
 
@@ -336,6 +338,7 @@ var p = newParser("sc"):
         arg("fastq", nargs = 1, help = "Input FASTQ")
         run:
             fq_dedup.fq_dedup(opts.fastq)
+    
     command("json", group="VCF"):
         help("Convert a VCF to JSON")
         arg("vcf", nargs = 1, help="VCF to convert to JSON")
@@ -351,6 +354,17 @@ var p = newParser("sc"):
         flag("--debug", help="Debug")
         run:
             to_json(get_vcf(opts.vcf), opts.region, opts.samples, opts.info, opts.format, opts.zip, opts.annotation, opts.pretty, opts.array, opts.pass)
+    
+    command("vcf2tsv", group="VCF"):
+        help("Converts a VCF to TSV or CSV")
+        flag("--header", help="Output the header")
+        arg("vcf", nargs = 1, help = "Input FASTQ")
+        run:
+            if opts.vcf.len == 0:
+                quit_error("No VCF specified", 3)
+            elif opts.vcf.len > 0:
+                vcf2tsv(opts.vcf)
+    
     command("fasta", group="VCF"):
         help("Convert a VCF to a FASTA file")
         arg("vcf", nargs = 1, help="VCF to convert to JSON")
diff --git a/src/fq_count.nim b/src/fq_count.nim
index dad45e8..e888cb5 100644
--- a/src/fq_count.nim
+++ b/src/fq_count.nim
@@ -6,11 +6,13 @@ import strformat
 import strutils
 import os
 
-const header* = ["reads",
-                "gc_content",
-                "gc_bases",
-                "bases",
-                "fname"].join("\t")
+const fq_count_header* = ["reads",
+                          "gc_content",
+                          "gc_bases",
+                          "n_bases",
+                          "bases",
+                          "basename",
+                          "absolute_path"].join("\t")
 
 
 
diff --git a/tasks.todo b/tasks.todo
index 52bd397..73bafcd 100644
--- a/tasks.todo
+++ b/tasks.todo
@@ -33,4 +33,14 @@ Index Swap:
   ☐ Minimum coverage level (10 reads)
   ☐ Group by flowcell/lane
 
+BAM:
+    ☐ BAM list chromoomes
+    ☐ BAM window iterator
+    ☐ Tajima's D (Parallelize across chrom?)
+
+VCF:
+    ☐ VCF list chromosome
+    ☐ VCF window iterator
+    ☐ VCF Subsample?
+
 Genome manager (a better one?):