Commit 15dea386 authored by aknecht2's avatar aknecht2
Browse files

Updated workflow_job validation. Added rawfile type. Added gem wrapper...

Updated workflow_job validation.  Added rawfile type.  Added gem wrapper script, yaml, and chromsome conversion script.
parent 10f026fd
......@@ -51,6 +51,8 @@ file_extensions = {
"xls": ["xls"],
"yaml": ["yaml"],
"result": ["bed", "narrowPeak", "broadPeak", "tagAlign"],
"txt": ["txt"],
"chrom_sizes": ["sizes"]
}
# list of resources that can be specified per job (step) in
......@@ -76,18 +78,33 @@ resources = {
# Defines the types of input / output arguments
# argument -> Any non file argument
# string -> Any string argument
# numeric -> Numeric arguments.
# file -> Any file argument that isn't redirected
# stdout -> Any file argument that is redirected from stdout
# stderr -> Any file argument that is redirected from stderr
# file -> Normal file arguments.
# stdout -> Any file argument that is redirected from stdout
# stderr -> Any file argument that is redirected from stderr
argument_types = {
"argument": ["argument"],
"file": ["file", "stdout", "stderr"]
"argument": ["string", "numeric"],
"file": ["file", "rawfile", "stdout", "stderr"]
}
# Defines information about arguments
argument_keys = {
"required": ["type", "changeable", "has_value"],
"optional": ["required", "default"]
}
# workflow_job keys
job_keys = {
"required": ["inputs", "additional_inputs", "outputs", "command", "arguments"] + resources.keys(),
"optional": []
}
# param keys
param_keys = {
"required": ["arguments"],
"optional": resources.keys()
"required": [],
"optional": ["arguments"] + resources.keys()
}
# workflow order
......
......@@ -33,3 +33,11 @@ remove_duplicates:
outputs:
- no_dups.bed:
type: stdout
- chr_locus_convert.yaml:
inputs:
- no_dups.bed:
type: file
additional_inputs: null
outputs:
- no_dups_chr.bed:
type: file
db_save_result:
inputs:
- bed:
type: file
additional_inputs: null
outputs:
- bed:
type: file
command: db_save_result.py
arguments:
- "-b":
changeable: false
required: true
has_value: true
default: $inputs.0
- "-o":
changeable: false
required: true
has_value: true
default: $outputs.0
walltime: 120
memory: 4000
cores: 1
nodes: 1
gem_callpeak:
inputs:
- txt:
type: rawfile
- chrom_sizes:
type: file
- bed:
type: file
- bed:
type: file
- genome:
type: argument
- prefix:
type: argument
additional_inputs: null
outputs:
- peak:
type: file
command: gem
arguments:
- "--d":
type: file
changeable: true
required: true
has_value: true
default: $inputs.0
- "--g":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
- "--expt":
type: file
changeable: false
required: true
has_value: true
default: $inputs.2
- "--ctrl":
type: file
changeable: false
required: true
has_value: true
defualt: $inputs.3
- "--genome":
type: file
changeable: false
required: true
has_value: true
default: $inputs.4
- "--out":
type: argument
changeable: false
required: true
has_value: true
default: $inputs.5
- "--k_min":
type: numeric
changeable: true
required: true
has_value: true
default: 6
- "--k_max":
type: numeric
changeable: true
required: false
has_value: true
default: 13
- "--q":
type: numeric
changeable: true
required: false
has_value: true
default: 1
- "--t":
type: numeric
changeable: true
required: false
has_value: true
default: 2
- "--outNP":
type: boolean
changeable: false
required: false
has_value: false
walltime: 720
memory: 16000
cores: 2
nodes: 1
import pymysql
import argparse
import os
parser = argparse.ArgumentParser(description="Replace chromosome locus with number.")
parser.add_argument("-b", "--bed", dest="bed", required=True, help="Input bed file.")
parser.add_argument("-o", "--out", dest="out", required=True, help="Output file.")
parser.add_argument("-c", "--c", dest="chr", default=False, action="store_true", help="If specified convert from name to chr number, otherwise convert from chr number to name.")
parser.add_argument("-d", "--db", dest="db", default="hg38", help="Database to load conversion from.")
parser.add_argument("-s", "--server", dest="server", default="genome-mysql.cse.ucsc.edu", help="Location of mysql server.")
parser.add_argument("-u", "--user", dest="user", default="genome", help="Username for db login.")
parser.add_argument("-p", "--password", dest="password", default="", help="Password for db login.")
parser.add_argument("-t", "--table", dest="table", default="ucscToINSDC", help="Table to retrieve locus -> number info from.")
args = parser.parse_args()
if os.path.isfile(args.bed):
# Setup connection, retrieve all info
conn = pymysql.connect(host=args.server, user=args.user, password=args.password, db=args.db, cursorclass=pymysql.cursors.DictCursor)
with conn.cursor() as cursor:
cursor.execute("SELECT * FROM %s" % (args.table,))
conn.commit()
results = cursor.fetchall()
# Results are a list of dictionaries ->
# [{"name": "CM000663.2", "chrom": "chr1"}, ...]
# Convert to a single dictionary with comprehension
# depending on directionality of the conversion
chr_map = dict([
(row["name"], row["chrom"]) if args.chr else (row["chrom"], row["name"])
for row in results
])
# Read in the input file, write the output file
with open(args.bed, "r") as rh:
with open(args.out, "w") as wh:
for line in rh.readlines():
# Bed is a 6 column format
bed_data = line.split()
if bed_data[0] in chr_map:
bed_data[0] = chr_map[bed_data[0]]
# Convert back from array to lines
wh.write("\t".join(bed_data) + "\n")
else:
print "Input file %s does not exist." % (args.bed,)
chr1 10156 10192 ILLUMINA-EAS45_4:10:21:17425:9246:0:1:1 31 -
chr1 16085 16121 ILLUMINA-EAS45_4:10:65:15288:19407:0:1:1 31 -
chr1 16209 16245 ILLUMINA-EAS45_4:10:71:11512:18151:0:1:1 31 +
chr1 16214 16250 ILLUMINA-EAS45_4:10:69:9718:1469:0:1:1 31 -
chr1 16292 16328 ILLUMINA-EAS45_4:10:16:10396:12291:0:1:1 31 -
chr1 17470 17506 ILLUMINA-EAS45_4:10:107:13943:1438:0:1:1 35 +
chr1 52035 52071 ILLUMINA-EAS45_4:10:111:16911:20203:0:1:1 31 +
chr1 56453 56489 ILLUMINA-EAS45_4:10:29:10212:2358:0:1:1 31 +
chr1 58786 58822 ILLUMINA-EAS45_4:10:120:15723:20738:0:1:1 31 -
chr1 59025 59061 ILLUMINA-EAS45_4:10:61:7767:18212:0:1:1 31 +
chr1 62163 62199 ILLUMINA-EAS45_4:10:81:10371:7594:0:1:1 42 +
chr1 69558 69594 ILLUMINA-EAS45_4:10:10:15951:7741:0:1:1 31 +
chr1 77105 77141 ILLUMINA-EAS45_4:10:16:15838:10961:0:1:1 31 +
chr1 79585 79621 ILLUMINA-EAS45_4:10:31:15325:5400:0:1:1 31 -
chr1 82635 82671 ILLUMINA-EAS45_4:10:117:10450:20899:0:1:1 31 -
chr1 82708 82744 ILLUMINA-EAS45_4:10:37:12603:13930:0:1:1 31 +
chr1 86070 86106 ILLUMINA-EAS45_4:10:75:15948:19373:0:1:1 31 -
chr1 87949 87985 ILLUMINA-EAS45_4:10:86:12777:16822:0:1:1 31 -
chr1 88354 88390 ILLUMINA-EAS45_4:10:40:16842:7075:0:1:1 31 +
chr1 93278 93314 ILLUMINA-EAS45_4:10:102:2128:8520:0:1:1 31 +
chr1 96581 96617 ILLUMINA-EAS45_4:10:11:17897:18562:0:1:1 31 +
chr1 96583 96619 ILLUMINA-EAS45_4:10:64:6470:7060:0:1:1 31 -
chr1 106798 106834 ILLUMINA-EAS45_4:10:54:13448:13431:0:1:1 31 -
chr1 120220 120256 ILLUMINA-EAS45_4:10:42:15212:18079:0:1:1 31 -
chr1 120249 120285 ILLUMINA-EAS45_4:10:44:8552:17683:0:1:1 31 +
chr1 122846 122882 ILLUMINA-EAS45_4:10:9:10228:20532:0:1:1 40 +
chr1 125380 125416 ILLUMINA-EAS45_4:10:37:6089:9670:0:1:1 31 -
chr1 126148 126184 ILLUMINA-EAS45_4:10:3:1970:1708:0:1:1 31 +
chr1 127524 127560 ILLUMINA-EAS45_4:10:70:4160:14245:0:1:1 31 +
chr1 128640 128676 ILLUMINA-EAS45_4:10:34:7239:18333:0:1:1 31 +
chr1 128716 128752 ILLUMINA-EAS45_4:10:117:19323:14404:0:1:1 31 -
chr1 133406 133442 ILLUMINA-EAS45_4:10:50:11699:9351:0:1:1 31 -
chr1 137782 137818 ILLUMINA-EAS45_4:10:57:11060:18224:0:1:1 31 +
chr1 144899 144935 ILLUMINA-EAS45_4:10:114:9239:9270:0:1:1 31 -
chr1 180746 180782 ILLUMINA-EAS45_4:10:104:7020:9868:0:1:1 31 +
chr1 180790 180826 ILLUMINA-EAS45_4:10:42:17029:2428:0:1:1 31 +
chr1 182012 182048 ILLUMINA-EAS45_4:10:65:9106:15166:0:1:1 31 -
chr1 184459 184495 ILLUMINA-EAS45_4:10:88:14748:6331:0:1:1 42 -
chr1 186825 186861 ILLUMINA-EAS45_4:10:94:14095:17782:0:1:1 31 +
chr1 186866 186902 ILLUMINA-EAS45_4:10:19:9482:3268:0:1:1 31 +
chr1 191032 191068 ILLUMINA-EAS45_4:10:110:1476:14010:0:1:1 31 +
chr1 191330 191366 ILLUMINA-EAS45_4:10:8:19815:6561:0:1:1 31 +
chr1 261997 262033 ILLUMINA-EAS45_4:10:114:8651:17849:0:1:1 31 +
chr1 262715 262751 ILLUMINA-EAS45_4:10:110:1291:3125:0:1:1 31 -
chr1 264674 264710 ILLUMINA-EAS45_4:10:4:13875:8818:0:1:1 31 -
chr1 267970 268006 ILLUMINA-EAS45_4:10:50:5101:3057:0:1:1 31 +
chr1 267977 268013 ILLUMINA-EAS45_4:10:34:1506:10692:0:1:1 31 +
chr1 267983 268019 ILLUMINA-EAS45_4:10:45:3903:12330:0:1:1 31 +
chr1 268438 268474 ILLUMINA-EAS45_4:10:7:8311:2869:0:1:1 31 +
chr1 268501 268537 ILLUMINA-EAS45_4:10:100:14883:13903:0:1:1 31 +
chr1 268518 268554 ILLUMINA-EAS45_4:10:76:3270:10518:0:1:1 31 -
chr1 270693 270729 ILLUMINA-EAS45_4:10:65:18005:6231:0:1:1 31 -
chr1 273905 273941 ILLUMINA-EAS45_4:10:79:4360:11889:0:1:1 31 -
chr1 274397 274433 ILLUMINA-EAS45_4:10:43:14007:11437:0:1:1 31 -
chr1 276290 276326 ILLUMINA-EAS45_4:10:59:9478:7683:0:1:1 31 +
chr1 279256 279292 ILLUMINA-EAS45_4:10:19:10551:3406:0:1:1 31 +
chr1 281363 281399 ILLUMINA-EAS45_4:10:22:18865:20154:0:1:0 31 +
chr1 281371 281407 ILLUMINA-EAS45_4:10:77:3406:20771:0:1:1 31 +
chr1 281859 281895 ILLUMINA-EAS45_4:10:35:15202:13583:0:1:1 31 -
chr1 284329 284365 ILLUMINA-EAS45_4:10:116:8491:11510:0:1:1 31 +
chr1 288905 288941 ILLUMINA-EAS45_4:10:63:5047:3717:0:1:1 31 -
chr1 289433 289469 ILLUMINA-EAS45_4:10:24:5928:11680:0:1:1 40 -
chr1 291810 291846 ILLUMINA-EAS45_4:10:79:7725:4321:0:1:1 31 +
chr1 297536 297572 ILLUMINA-EAS45_4:10:59:16132:2005:0:1:1 31 +
chr1 509436 509472 ILLUMINA-EAS45_4:10:54:12910:15282:0:1:1 31 +
chr1 511660 511696 ILLUMINA-EAS45_4:10:5:7558:1706:0:1:1 31 -
chr1 516589 516625 ILLUMINA-EAS45_4:10:77:13748:8619:0:1:1 31 +
chr1 525096 525132 ILLUMINA-EAS45_4:10:109:2411:2534:0:1:1 31 -
chr1 526743 526779 ILLUMINA-EAS45_4:10:105:19554:8986:0:1:1 31 -
chr1 531155 531191 ILLUMINA-EAS45_4:10:11:5889:17692:0:1:1 31 +
chr1 533774 533810 ILLUMINA-EAS45_4:10:80:19344:11717:0:1:1 31 +
chr1 591168 591204 ILLUMINA-EAS45_4:10:114:19794:16457:0:1:1 31 +
chr1 591169 591205 ILLUMINA-EAS45_4:10:119:12527:18471:0:1:1 31 -
chr1 591350 591386 ILLUMINA-EAS45_4:10:109:11715:10684:0:1:1 31 +
chr1 591788 591824 ILLUMINA-EAS45_4:10:88:8653:2536:0:1:1 31 -
chr1 597750 597786 ILLUMINA-EAS45_4:10:46:9393:12090:0:1:1 32 -
chr1 603507 603543 ILLUMINA-EAS45_4:10:8:10579:11116:0:1:1 31 +
chr1 603517 603553 ILLUMINA-EAS45_4:10:100:13723:17986:0:1:1 31 +
chr1 603522 603558 ILLUMINA-EAS45_4:10:83:16210:1015:0:1:1 42 -
chr1 605578 605614 ILLUMINA-EAS45_4:10:37:6324:12178:0:1:1 31 -
chr1 609128 609164 ILLUMINA-EAS45_4:10:82:7426:15461:0:1:1 31 +
chr1 609338 609374 ILLUMINA-EAS45_4:10:64:13784:10330:0:1:1 31 -
chr1 612974 613010 ILLUMINA-EAS45_4:10:71:12695:3519:0:1:1 31 +
chr1 613088 613124 ILLUMINA-EAS45_4:10:80:14090:7941:0:1:1 31 +
chr1 613090 613126 ILLUMINA-EAS45_4:10:5:18877:20621:0:1:1 31 +
chr1 627499 627535 ILLUMINA-EAS45_4:10:86:11145:6432:0:1:1 31 -
chr1 629060 629096 ILLUMINA-EAS45_4:10:42:3539:4395:0:1:1 42 +
chr1 629595 629631 ILLUMINA-EAS45_4:10:85:7505:14939:0:1:1 31 -
chr1 629905 629941 ILLUMINA-EAS45_4:10:41:3894:1917:0:1:1 35 -
chr1 629906 629942 ILLUMINA-EAS45_4:10:100:1219:7398:0:1:1 31 +
chr1 629906 629942 ILLUMINA-EAS45_4:10:117:13273:7805:0:1:1 31 -
chr1 629907 629943 ILLUMINA-EAS45_4:10:62:6557:6527:0:1:1 31 +
chr1 629907 629943 ILLUMINA-EAS45_4:10:9:14497:3249:0:1:1 31 -
chr1 629908 629944 ILLUMINA-EAS45_4:10:119:5487:8356:0:1:1 31 +
chr1 629908 629944 ILLUMINA-EAS45_4:10:33:13375:16342:0:1:1 31 -
chr1 629909 629945 ILLUMINA-EAS45_4:10:6:8915:13373:0:1:1 31 +
chr1 629909 629945 ILLUMINA-EAS45_4:10:113:4640:10892:0:1:1 31 -
chr1 629910 629946 ILLUMINA-EAS45_4:10:120:5972:7258:0:1:1 31 +
chr1 629910 629946 ILLUMINA-EAS45_4:10:116:8227:18746:0:1:1 31 -
chr1 629911 629947 ILLUMINA-EAS45_4:10:13:2582:9971:0:1:1 31 +
chr1 629911 629947 ILLUMINA-EAS45_4:10:18:4161:4433:0:1:1 31 -
chr1 629912 629948 ILLUMINA-EAS45_4:10:37:8037:10004:0:1:1 31 +
chr1 629912 629948 ILLUMINA-EAS45_4:10:100:2435:9062:0:1:1 31 -
chr1 629913 629949 ILLUMINA-EAS45_4:10:16:8350:5059:0:1:1 31 +
chr1 629913 629949 ILLUMINA-EAS45_4:10:35:16802:13269:0:1:1 31 -
chr1 629914 629950 ILLUMINA-EAS45_4:10:21:11188:18959:0:1:1 31 +
chr1 629914 629950 ILLUMINA-EAS45_4:10:83:6490:8081:0:1:1 31 -
chr1 629915 629951 ILLUMINA-EAS45_4:10:87:6230:14656:0:1:1 31 +
chr1 629915 629951 ILLUMINA-EAS45_4:10:43:16623:8200:0:1:1 31 -
chr1 629916 629952 ILLUMINA-EAS45_4:10:62:13505:13342:0:1:1 31 +
chr1 629916 629952 ILLUMINA-EAS45_4:10:73:15959:13647:0:1:1 31 -
chr1 629917 629953 ILLUMINA-EAS45_4:10:114:18391:17021:0:1:1 31 +
chr1 629917 629953 ILLUMINA-EAS45_4:10:83:11858:5537:0:1:1 31 -
chr1 629918 629954 ILLUMINA-EAS45_4:10:37:3248:18433:0:1:1 31 +
chr1 629918 629954 ILLUMINA-EAS45_4:10:44:13095:6065:0:1:1 31 -
chr1 629919 629955 ILLUMINA-EAS45_4:10:3:7616:5538:0:1:1 31 +
chr1 629919 629955 ILLUMINA-EAS45_4:10:19:6295:4913:0:1:1 31 -
chr1 629920 629956 ILLUMINA-EAS45_4:10:105:3022:15194:0:1:1 31 +
chr1 629920 629956 ILLUMINA-EAS45_4:10:113:3566:4161:0:1:1 31 -
chr1 629921 629957 ILLUMINA-EAS45_4:10:45:1834:6614:0:1:1 31 +
chr1 629921 629957 ILLUMINA-EAS45_4:10:22:11487:8320:0:1:1 31 -
chr1 629922 629958 ILLUMINA-EAS45_4:10:103:7510:15478:0:1:1 31 +
chr1 629922 629958 ILLUMINA-EAS45_4:10:112:9219:4400:0:1:1 31 -
chr1 629923 629959 ILLUMINA-EAS45_4:10:113:8889:3858:0:1:1 31 +
chr1 629923 629959 ILLUMINA-EAS45_4:10:14:7884:7145:0:1:1 31 -
chr1 629924 629960 ILLUMINA-EAS45_4:10:116:7321:2659:0:1:1 31 +
chr1 629924 629960 ILLUMINA-EAS45_4:10:54:3264:18281:0:1:1 31 -
chr1 629925 629961 ILLUMINA-EAS45_4:10:44:6370:1639:0:1:1 31 +
chr1 629925 629961 ILLUMINA-EAS45_4:10:52:17300:7003:0:1:1 31 -
chr1 629926 629962 ILLUMINA-EAS45_4:10:6:5981:15795:0:1:1 31 +
chr1 629926 629962 ILLUMINA-EAS45_4:10:10:12868:16163:0:1:1 31 -
chr1 629927 629963 ILLUMINA-EAS45_4:10:118:13937:1228:0:1:1 31 +
chr1 629927 629963 ILLUMINA-EAS45_4:10:14:10007:15603:0:1:1 31 -
chr1 629928 629964 ILLUMINA-EAS45_4:10:103:3823:18262:0:1:1 31 +
chr1 629928 629964 ILLUMINA-EAS45_4:10:109:8734:12792:0:1:1 31 -
chr1 629929 629965 ILLUMINA-EAS45_4:10:47:12586:17804:0:1:1 31 +
chr1 629929 629965 ILLUMINA-EAS45_4:10:59:10947:8256:0:1:1 31 -
chr1 629930 629966 ILLUMINA-EAS45_4:10:115:10788:3388:0:1:1 31 +
chr1 629930 629966 ILLUMINA-EAS45_4:10:39:13835:18313:0:1:1 31 -
chr1 629931 629967 ILLUMINA-EAS45_4:10:104:17465:11233:0:1:1 31 +
chr1 629931 629967 ILLUMINA-EAS45_4:10:41:7321:2119:0:1:1 31 -
chr1 629932 629968 ILLUMINA-EAS45_4:10:107:14212:20106:0:1:1 31 +
chr1 629932 629968 ILLUMINA-EAS45_4:10:118:15067:3550:0:1:1 31 -
chr1 629933 629969 ILLUMINA-EAS45_4:10:2:13252:5295:0:1:1 31 +
chr1 629933 629969 ILLUMINA-EAS45_4:10:102:7881:16909:0:1:1 31 -
chr1 629934 629970 ILLUMINA-EAS45_4:10:59:5428:2504:0:1:1 31 +
chr1 629934 629970 ILLUMINA-EAS45_4:10:114:16485:15896:0:1:1 31 -
chr1 629935 629971 ILLUMINA-EAS45_4:10:10:8997:10980:0:1:1 31 +
chr1 629935 629971 ILLUMINA-EAS45_4:10:11:12525:16308:0:1:1 31 -
chr1 629936 629972 ILLUMINA-EAS45_4:10:10:11767:2354:0:1:1 31 +
chr1 629936 629972 ILLUMINA-EAS45_4:10:17:15856:4532:0:1:1 31 -
chr1 629937 629973 ILLUMINA-EAS45_4:10:34:15567:16740:0:1:1 31 +
chr1 629937 629973 ILLUMINA-EAS45_4:10:119:14242:4623:0:1:1 31 -
chr1 629938 629974 ILLUMINA-EAS45_4:10:115:12522:15229:0:1:1 31 +
chr1 629938 629974 ILLUMINA-EAS45_4:10:19:17731:17294:0:1:1 31 -
chr1 630177 630213 ILLUMINA-EAS45_4:10:90:5654:10917:0:1:1 40 +
chr1 630193 630229 ILLUMINA-EAS45_4:10:62:8861:16907:0:1:1 31 +
chr1 630291 630327 ILLUMINA-EAS45_4:10:96:7923:3529:0:1:1 40 -
chr1 630315 630351 ILLUMINA-EAS45_4:10:4:4275:10890:0:1:1 31 +
chr1 630481 630517 ILLUMINA-EAS45_4:10:61:2679:7122:0:1:1 31 +
chr1 630523 630559 ILLUMINA-EAS45_4:10:90:7256:5585:0:1:1 40 +
chr1 630552 630588 ILLUMINA-EAS45_4:10:29:7936:20570:0:1:1 31 -
chr1 630564 630600 ILLUMINA-EAS45_4:10:29:18413:12107:0:1:1 31 +
chr1 630652 630688 ILLUMINA-EAS45_4:10:75:8257:7333:0:1:1 31 -
chr1 630666 630702 ILLUMINA-EAS45_4:10:30:8444:7708:0:1:1 31 -
chr1 630667 630703 ILLUMINA-EAS45_4:10:92:14240:9403:0:1:1 40 +
chr1 631164 631200 ILLUMINA-EAS45_4:10:56:9383:10217:0:1:1 31 +
chr1 631177 631213 ILLUMINA-EAS45_4:10:71:9353:4938:0:1:1 31 -
chr1 631183 631219 ILLUMINA-EAS45_4:10:106:8091:17382:0:1:1 31 -
chr1 631357 631393 ILLUMINA-EAS45_4:10:24:10602:20496:0:1:1 40 -
chr1 631395 631431 ILLUMINA-EAS45_4:10:20:12429:4978:0:1:1 40 +
chr1 631636 631672 ILLUMINA-EAS45_4:10:90:19645:18175:0:1:0 31 -
chr1 631660 631696 ILLUMINA-EAS45_4:10:72:9309:7886:0:1:1 31 -
chr1 632070 632106 ILLUMINA-EAS45_4:10:16:7260:14070:0:1:1 31 +
chr1 632070 632106 ILLUMINA-EAS45_4:10:1:18980:8816:0:1:1 31 -
chr1 632072 632108 ILLUMINA-EAS45_4:10:23:12646:17141:0:1:1 31 +
chr1 632072 632108 ILLUMINA-EAS45_4:10:3:2317:12509:0:1:1 31 -
chr1 632469 632505 ILLUMINA-EAS45_4:10:101:13274:11972:0:1:1 31 +
chr1 632483 632519 ILLUMINA-EAS45_4:10:28:19678:17603:0:1:1 31 -
chr1 632841 632877 ILLUMINA-EAS45_4:10:119:16847:18636:0:1:1 31 -
chr1 633010 633046 ILLUMINA-EAS45_4:10:15:4434:14498:0:1:1 31 +
chr1 633160 633196 ILLUMINA-EAS45_4:10:73:14046:3036:0:1:1 31 +
chr1 633328 633364 ILLUMINA-EAS45_4:10:39:1409:4087:0:1:0 40 +
chr1 633637 633673 ILLUMINA-EAS45_4:10:32:1799:17004:0:1:1 31 +
chr1 633682 633718 ILLUMINA-EAS45_4:10:29:4043:5995:0:1:1 31 +
chr1 633707 633743 ILLUMINA-EAS45_4:10:56:13525:11957:0:1:1 31 -
chr1 633875 633911 ILLUMINA-EAS45_4:10:53:11273:19748:0:1:0 31 +
chr1 633993 634029 ILLUMINA-EAS45_4:10:7:12470:16606:0:1:1 31 +
chr1 633993 634029 ILLUMINA-EAS45_4:10:111:3224:11873:0:1:1 31 -
chr1 633994 634030 ILLUMINA-EAS45_4:10:17:13003:17506:0:1:1 31 +
chr1 633994 634030 ILLUMINA-EAS45_4:10:112:18665:14492:0:1:1 31 -
chr1 633995 634031 ILLUMINA-EAS45_4:10:120:13440:9796:0:1:1 31 +
chr1 633995 634031 ILLUMINA-EAS45_4:10:14:17150:18542:0:1:1 31 -
chr1 633996 634032 ILLUMINA-EAS45_4:10:118:17751:14363:0:1:1 31 +
chr1 633996 634032 ILLUMINA-EAS45_4:10:22:13191:6752:0:1:1 31 -
chr1 633997 634033 ILLUMINA-EAS45_4:10:65:12292:11845:0:1:1 31 +
chr1 633997 634033 ILLUMINA-EAS45_4:10:116:4277:2564:0:1:1 31 -
chr1 633998 634034 ILLUMINA-EAS45_4:10:1:18514:17377:0:1:1 31 +
chr1 633998 634034 ILLUMINA-EAS45_4:10:36:15479:7888:0:1:1 31 -
chr1 633999 634035 ILLUMINA-EAS45_4:10:13:2559:14734:0:1:1 31 +
chr1 633999 634035 ILLUMINA-EAS45_4:10:55:12776:18709:0:1:1 31 -
chr1 634000 634036 ILLUMINA-EAS45_4:10:115:14961:14787:0:1:1 31 +
chr1 634000 634036 ILLUMINA-EAS45_4:10:113:14192:13588:0:1:1 31 -
chr1 634001 634037 ILLUMINA-EAS45_4:10:6:16326:2629:0:1:1 31 +
chr1 634001 634037 ILLUMINA-EAS45_4:10:42:10311:6395:0:1:1 31 -
chr1 634002 634038 ILLUMINA-EAS45_4:10:48:14090:14263:0:1:1 31 +
chr1 634002 634038 ILLUMINA-EAS45_4:10:59:6618:6891:0:1:1 31 -
chr1 634003 634039 ILLUMINA-EAS45_4:10:6:9848:2824:0:1:1 31 +
chr1 634003 634039 ILLUMINA-EAS45_4:10:2:14730:10261:0:1:1 31 -
chr1 634004 634040 ILLUMINA-EAS45_4:10:81:7957:12899:0:1:1 31 +
chr1 634004 634040 ILLUMINA-EAS45_4:10:17:6196:4128:0:1:1 31 -
chr1 634005 634041 ILLUMINA-EAS45_4:10:20:11476:5583:0:1:1 31 +
chr1 634005 634041 ILLUMINA-EAS45_4:10:104:11937:10546:0:1:1 31 -
chr1 634006 634042 ILLUMINA-EAS45_4:10:104:13338:16163:0:1:1 31 +
chr1 634006 634042 ILLUMINA-EAS45_4:10:108:8755:12854:0:1:1 31 -
chr1 634007 634043 ILLUMINA-EAS45_4:10:68:14214:7761:0:1:1 31 +
chr1 634007 634043 ILLUMINA-EAS45_4:10:50:6206:9828:0:1:1 31 -
chr1 634008 634044 ILLUMINA-EAS45_4:10:73:13409:7380:0:1:1 31 +
chr1 634008 634044 ILLUMINA-EAS45_4:10:16:15920:7361:0:1:1 31 -
chr1 634009 634045 ILLUMINA-EAS45_4:10:42:14181:5105:0:1:1 31 +
chr1 634009 634045 ILLUMINA-EAS45_4:10:104:14650:6860:0:1:1 31 -
chr1 634010 634046 ILLUMINA-EAS45_4:10:101:10165:9152:0:1:1 31 +
chr1 634010 634046 ILLUMINA-EAS45_4:10:64:8370:15937:0:1:1 31 -
chr1 634011 634047 ILLUMINA-EAS45_4:10:5:15064:6602:0:1:1 31 +
chr1 634011 634047 ILLUMINA-EAS45_4:10:77:11369:10778:0:1:1 31 -
chr1 634012 634048 ILLUMINA-EAS45_4:10:47:12854:7257:0:1:1 31 +
chr1 634012 634048 ILLUMINA-EAS45_4:10:105:9229:11291:0:1:1 31 -
chr1 634013 634049 ILLUMINA-EAS45_4:10:63:4653:9335:0:1:1 31 +
chr1 634013 634049 ILLUMINA-EAS45_4:10:23:11238:12480:0:1:1 31 -
chr1 634014 634050 ILLUMINA-EAS45_4:10:59:10480:4917:0:1:1 31 +
chr1 634014 634050 ILLUMINA-EAS45_4:10:71:4723:16161:0:1:1 31 -
chr1 634015 634051 ILLUMINA-EAS45_4:10:103:10991:18631:0:1:1 31 +
chr1 634015 634051 ILLUMINA-EAS45_4:10:64:11551:2619:0:1:1 31 -
chr1 634016 634052 ILLUMINA-EAS45_4:10:22:5364:14191:0:1:1 31 +
chr1 634016 634052 ILLUMINA-EAS45_4:10:4:8877:8291:0:1:1 31 -
chr1 634017 634053 ILLUMINA-EAS45_4:10:112:11585:8996:0:1:1 31 +
chr1 634017 634053 ILLUMINA-EAS45_4:10:80:15833:19142:0:1:1 31 -
chr1 634018 634054 ILLUMINA-EAS45_4:10:43:14305:13080:0:1:1 31 +
chr1 634018 634054 ILLUMINA-EAS45_4:10:6:8526:9204:0:1:1 31 -
chr1 634019 634055 ILLUMINA-EAS45_4:10:10:4209:11095:0:1:1 31 +
chr1 634019 634055 ILLUMINA-EAS45_4:10:38:15602:14952:0:1:1 31 -
chr1 634020 634056 ILLUMINA-EAS45_4:10:51:11094:16382:0:1:1 31 +
chr1 634020 634056 ILLUMINA-EAS45_4:10:2:16577:18249:0:1:1 31 -
chr1 634021 634057 ILLUMINA-EAS45_4:10:69:6783:10858:0:1:1 31 +
chr1 634021 634057 ILLUMINA-EAS45_4:10:106:9774:20834:0:1:1 31 -
chr1 634022 634058 ILLUMINA-EAS45_4:10:13:12849:12781:0:1:1 31 -
chr1 634023 634059 ILLUMINA-EAS45_4:10:36:13057:17095:0:1:1 31 +
chr1 634023 634059 ILLUMINA-EAS45_4:10:42:2667:10181:0:1:1 31 -
chr1 634024 634060 ILLUMINA-EAS45_4:10:48:11193:16275:0:1:1 31 +
chr1 634024 634060 ILLUMINA-EAS45_4:10:100:16921:8457:0:1:1 31 -
chr1 634025 634061 ILLUMINA-EAS45_4:10:87:11629:4628:0:1:1 31 +
chr1 634025 634061 ILLUMINA-EAS45_4:10:113:5953:18114:0:1:1 31 -
chr1 634026 634062 ILLUMINA-EAS45_4:10:62:16933:1793:0:1:1 31 +
chr1 634026 634062 ILLUMINA-EAS45_4:10:20:6742:8599:0:1:1 31 -
chr1 634027 634063 ILLUMINA-EAS45_4:10:10:6275:14540:0:1:1 31 +
chr1 634027 634063 ILLUMINA-EAS45_4:10:22:10556:5924:0:1:1 31 -
chr1 634028 634064 ILLUMINA-EAS45_4:10:11:7466:7632:0:1:1 31 +
chr1 634028 634064 ILLUMINA-EAS45_4:10:13:15716:4058:0:1:1 31 -
chr1 634086 634122 ILLUMINA-EAS45_4:10:96:11274:17047:0:1:1 40 -
chr1 634242 634278 ILLUMINA-EAS45_4:10:41:1267:2469:0:1:1 31 +
chr1 634326 634362 ILLUMINA-EAS45_4:10:42:5257:15745:0:1:1 31 +
chr1 634391 634427 ILLUMINA-EAS45_4:10:102:1793:5461:0:1:1 31 -
chr1 634399 634435 ILLUMINA-EAS45_4:10:78:13700:16588:0:1:1 31 -
chr1 634416 634452 ILLUMINA-EAS45_4:10:56:2011:4897:0:1:1 31 -
chr1 634421 634457 ILLUMINA-EAS45_4:10:32:6468:11213:0:1:1 31 -
chr1 634789 634825 ILLUMINA-EAS45_4:10:11:18093:7834:0:1:1 31 -
chr1 635251 635287 ILLUMINA-EAS45_4:10:22:13038:18863:0:1:1 31 -
chr1 636933 636969 ILLUMINA-EAS45_4:10:81:16826:13594:0:1:1 31 +
chr1 646037 646073 ILLUMINA-EAS45_4:10:104:15814:4502:0:1:1 31 -
chr1 646231 646267 ILLUMINA-EAS45_4:10:87:15133:11468:0:1:1 31 +
chr1 646979 647015 ILLUMINA-EAS45_4:10:120:16645:1493:0:1:1 31 +
chr1 654802 654838 ILLUMINA-EAS45_4:10:22:4956:17474:0:1:1 31 -
chr1 660522 660558 ILLUMINA-EAS45_4:10:68:14766:5055:0:1:1 31 +
chr1 662261 662297 ILLUMINA-EAS45_4:10:62:17220:9020:0:1:1 31 +
chr1 664878 664914 ILLUMINA-EAS45_4:10:99:5401:6503:0:1:1 31 -
chr1 665082 665118 ILLUMINA-EAS45_4:10:84:4136:10262:0:1:1 31 -
chr1 665462 665498 ILLUMINA-EAS45_4:10:4:8187:9121:0:1:1 31 +
chr1 665670 665706 ILLUMINA-EAS45_4:10:113:4883:16266:0:1:1 31 +
chr1 665681 665717 ILLUMINA-EAS45_4:10:103:17911:20298:0:1:1 31 +
chr1 668197 668233 ILLUMINA-EAS45_4:10:116:15237:6991:0:1:1 31 +
chr1 668322 668358 ILLUMINA-EAS45_4:10:84:16797:10617:0:1:1 31 -
chr1 668664 668700 ILLUMINA-EAS45_4:10:43:11444:16045:0:1:1 31 +
chr1 669430 669466 ILLUMINA-EAS45_4:10:19:1384:3336:0:1:1 31 +
chr1 674255 674291 ILLUMINA-EAS45_4:10:46:18893:12962:0:1:1 31 -
chr1 674264 674300 ILLUMINA-EAS45_4:10:83:19173:10005:0:1:1 31 -
chr1 683069 683105 ILLUMINA-EAS45_4:10:79:7336:2009:0:1:1 31 -
chr1 690027 690063 ILLUMINA-EAS45_4:10:111:3992:1454:0:1:1 31 -
chr1 690028 690064 ILLUMINA-EAS45_4:10:120:15675:1270:0:1:1 31 -
chr1 690029 690065 ILLUMINA-EAS45_4:10:113:16984:3706:0:1:1 31 +
chr1 690818 690854 ILLUMINA-EAS45_4:10:68:5962:6987:0:1:1 31 -
chr1 690940 690976 ILLUMINA-EAS45_4:10:5:1695:12108:0:1:1 31 +
chr1 692033 692069 ILLUMINA-EAS45_4:10:23:7648:12889:0:1:1 31 +
chr1 693163 693199 ILLUMINA-EAS45_4:10:37:1178:3425:0:1:1 31 -
chr1 708439 708475 ILLUMINA-EAS45_4:10:18:1177:20390:0:1:1 31 -
chr1 710214 710250 ILLUMINA-EAS45_4:10:18:18678:17541:0:1:1 31 +
chr1 714791 714827 ILLUMINA-EAS45_4:10:96:8666:19694:0:1:1 40 +
chr1 714807 714843 ILLUMINA-EAS45_4:10:2:10169:15894:0:1:1 31 -
chr1 715823 715859 ILLUMINA-EAS45_4:10:113:1694:2155:0:1:1 39 +
chr1 716221 716257 ILLUMINA-EAS45_4:10:63:13340:10822:0:1:1 31 +
chr1 717289 717325 ILLUMINA-EAS45_4:10:110:6465:19857:0:1:1 31 +
chr1 717305 717341 ILLUMINA-EAS45_4:10:112:17532:10111:0:1:1 31 -
chr1 718312 718348 ILLUMINA-EAS45_4:10:10:11784:10466:0:1:1 31 +
chr1 722599 722635 ILLUMINA-EAS45_4:10:12:14878:11006:0:1:1 31 -
chr1 727193 727229 ILLUMINA-EAS45_4:10:86:13046:20098:0:1:1 31 -
chr1 727244 727280 ILLUMINA-EAS45_4:10:63:15862:9863:0:1:1 31 -
chr1 729925 729961 ILLUMINA-EAS45_4:10:33:10649:7991:0:1:1 31 -
chr1 737715 737751 ILLUMINA-EAS45_4:10:106:1552:13199:0:1:1 31 -
chr1 740733 740769 ILLUMINA-EAS45_4:10:118:4653:1964:0:1:1 31 -
chr1 749348 749384 ILLUMINA-EAS45_4:10:7:11542:11603:0:1:1 31 +
chr1 773714 773750 ILLUMINA-EAS45_4:10:88:5538:5811:0:1:1 31 +
chr1 774800 774836 ILLUMINA-EAS45_4:10:80:11337:12110:0:1:1 31 -
chr1 775460 775496 ILLUMINA-EAS45_4:10:44:12083:11756:0:1:1 31 -
chr1 775792 775828 ILLUMINA-EAS45_4:10:39:3802:7338:0:1:1 31 +
chr1 777128 777164 ILLUMINA-EAS45_4:10:109:2947:11348:0:1:1 32 -
chr1 777365 777401 ILLUMINA-EAS45_4:10:119:17042:15511:0:1:1 35 +
chr1 777474 777510 ILLUMINA-EAS45_4:10:85:5391:15690:0:1:1 31 +
chr1 777483 777519 ILLUMINA-EAS45_4:10:120:1597:15698:0:1:1 31 -
chr1 777650 777686 ILLUMINA-EAS45_4:10:35:4787:13097:0:1:1 31 -
chr1 777885 777921 ILLUMINA-EAS45_4:10:6:14161:6116:0:1:1 31 +
chr1 778234 778270 ILLUMINA-EAS45_4:10:68:7962:15290:0:1:1 31 +
chr1 778521 778557 ILLUMINA-EAS45_4:10:29:3941:10849:0:1:1 42 -
chr1 778603 778639 ILLUMINA-EAS45_4:10:117:6995:18370:0:1:1 42 +
chr1 778615 778651 ILLUMINA-EAS45_4:10:41:15609:4023:0:1:1 42 +
chr1 778734 778770 ILLUMINA-EAS45_4:10:25:4948:9592:0:1:1 42 -
chr1 778779 778815 ILLUMINA-EAS45_4:10:6:18993:3985:0:1:1 31 +
chr1 778798 778834 ILLUMINA-EAS45_4:10:66:13918:14782:0:1:1 31 -
chr1 778809 778845 ILLUMINA-EAS45_4:10:48:2690:11466:0:1:1 31 -
chr1 778893 778929 ILLUMINA-EAS45_4:10:107:12198:7734:0:1:1 38 -
chr1 779786 779822 ILLUMINA-EAS45_4:10:66:7636:19215:0:1:1 31 +
chr1 779900 779936 ILLUMINA-EAS45_4:10:69:18608:18192:0:1:0 31 +
chr1 779991 780027 ILLUMINA-EAS45_4:10:36:4778:5617:0:1:1 42 +
chr1 780127 780163 ILLUMINA-EAS45_4:10:66:13985:9803:0:1:1 31 -
chr1 780340 780376 ILLUMINA-EAS45_4:10:22:11462:11184:0:1:1 31 -
chr1 780637 780673 ILLUMINA-EAS45_4:10:103:9241:18251:0:1:1 31 +
chr1 780836 780872 ILLUMINA-EAS45_4:10:101:14772:2680:0:1:1 31 -
chr1 782113 782149 ILLUMINA-EAS45_4:10:67:6027:6258:0:1:1 31 +
chr1 782182 782218 ILLUMINA-EAS45_4:10:82:1409:20486:0:1:1 31 -
chr1 782895 782931 ILLUMINA-EAS45_4:10:18:1294:20716:0:1:1 31 -
chr1 784346 784382 ILLUMINA-EAS45_4:10:53:15874:9162:0:1:1 31 +
chr1 784407 784443 ILLUMINA-EAS45_4:10:51:14243:2282:0:1:1 31 -
chr1 784478 784514 ILLUMINA-EAS45_4:10:45:14676:2235:0:1:1 31 -
chr1 784612 784648 ILLUMINA-EAS45_4:10:93:15619:2604:0:1:1 35 +
chr1 785262 785298 ILLUMINA-EAS45_4:10:95:4013:19674:0:1:1 32 +
chr1 785708 785744 ILLUMINA-EAS45_4:10:79:15747:20650:0:1:1 40 -
chr1 785881 785917 ILLUMINA-EAS45_4:10:17:10836:17191:0:1:1 35 -
chr1 785884 785920 ILLUMINA-EAS45_4:10:70:13773:15301:0:1:1 35 -
chr1 786357 786393 ILLUMINA-EAS45_4:10:38:2295:9635:0:1:1 31 -
chr1 786650 786686 ILLUMINA-EAS45_4:10:46:9618:17237:0:1:1 31 +
chr1 786688 786724 ILLUMINA-EAS45_4:10:29:16883:18352:0:1:1 31 -
chr1 786694 786730 ILLUMINA-EAS45_4:10:72:6898:15188:0:1:1 31 -
chr1 787268 787304 ILLUMINA-EAS45_4:10:33:17166:18553:0:1:1 31 +
chr1 787926 787962 ILLUMINA-EAS45_4:10:35:11214:9347:0:1:1 31 +
chr1 787943 787979 ILLUMINA-EAS45_4:10:4:3350:9424:0:1:1 31 -
chr1 787952 787988 ILLUMINA-EAS45_4:10:93:7038:3005:0:1:1 31 -
chr1 789186 789222 ILLUMINA-EAS45_4:10:116:6943:4992:0:1:1 31 +
chr1 789501 789537 ILLUMINA-EAS45_4:10:22:15485:17116:0:1:1 31 +
chr1 791282 791318 ILLUMINA-EAS45_4:10:58:19436:3067:0:1:1 35 -
chr1 791432 791468 ILLUMINA-EAS45_4:10:38:10958:5345:0:1:1 42 +
chr1 793738 793774 ILLUMINA-EAS45_4:10:46:10603:6133:0:1:1 31 +
chr1 793894 793930 ILLUMINA-EAS45_4:10:62:12983:12614:0:1:1 31 +
chr1 793955 793991 ILLUMINA-EAS45_4:10:15:3327:1762:0:1:1 31 +
chr1 794714 794750 ILLUMINA-EAS45_4:10:113:13132:9740:0:1:1 31 -
chr1 796280 796316 ILLUMINA-EAS45_4:10:42:7540:7237:0:1:1 31 -
chr1 796704 796740 ILLUMINA-EAS45_4:10:95:8701:5871:0:1:1 31 -
chr1 796744 796780 ILLUMINA-EAS45_4:10:72:1194:2821:0:1:1 31 -
chr1 797574 797610 ILLUMINA-EAS45_4:10:33:8970:16296:0:1:1 31 +
chr1 798735 798771 ILLUMINA-EAS45_4:10:12:9299:18799:0:1:1 31 -
chr1 799043 799079 ILLUMINA-EAS45_4:10:114:6059:11762:0:1:1 31 +
chr1 799187 799223 ILLUMINA-EAS45_4:10:23:12827:14617:0:1:1 35 +
chr1 799192 799228 ILLUMINA-EAS45_4:10:102:14077:2922:0:1:1 32 -
chr1 799207 799243 ILLUMINA-EAS45_4:10:107:16260:6410:0:1:1 31 +
chr1 799558 799594 ILLUMINA-EAS45_4:10:115:4113:19636:0:1:1 31 +
chr1 801449 801485 ILLUMINA-EAS45_4:10:13:19490:8087:0:1:1 31 -
chr1 801859 801895 ILLUMINA-EAS45_4:10:25:1999:7711:0:1:1 31 +
chr1 802795 802831 ILLUMINA-EAS45_4:10:38:14832:16880:0:1:1 31 +
chr1 803072 803108 ILLUMINA-EAS45_4:10:110:15685:15986:0:1:1 42 -
chr1 803921 803957 ILLUMINA-EAS45_4:10:73:7235:2683:0:1:1 31 -
chr1 803940 803976 ILLUMINA-EAS45_4:10:84:11630:1692:0:1:1 42 -
chr1 804902 804938 ILLUMINA-EAS45_4:10:42:15294:17409:0:1:1 31 +
chr1 804922 804958 ILLUMINA-EAS45_4:10:10:6854:5579:0:1:1 31 +
chr1 806598 806634 ILLUMINA-EAS45_4:10:108:8189:6894:0:1:1 31 +
chr1 806841 806877 ILLUMINA-EAS45_4:10:44:8770:7947:0:1:1 31 +
chr1 806899 806935 ILLUMINA-EAS45_4:10:84:14806:18350:0:1:1 31 -
chr1 807753 807789 ILLUMINA-EAS45_4:10:2:15927:4122:0:1:1 31 -
chr1 808187 808223 ILLUMINA-EAS45_4:10:38:6735:20730:0:1:1 31 +
chr1 811333 811369 ILLUMINA-EAS45_4:10:95:8177:9853:0:1:1 40 +
chr1 812111 812147 ILLUMINA-EAS45_4:10:107:15574:14556:0:1:1 31 +
chr1 812127 812163 ILLUMINA-EAS45_4:10:16:14469:6611:0:1:1 31 +
chr1 812325 812361 ILLUMINA-EAS45_4:10:116:1636:9505:0:1:1 31 +
chr1 812383 812419 ILLUMINA-EAS45_4:10:34:1334:8789:0:1:1 31 -
chr1 812732 812768 ILLUMINA-EAS45_4:10:95:14399:20978:0:1:1 31 +
chr1 812792 812828 ILLUMINA-EAS45_4:10:13:3655:4124:0:1:1 31 -
chr1 813016 813052 ILLUMINA-EAS45_4:10:42:18451:5275:0:1:1 31 +
chr1 816158 816194 ILLUMINA-EAS45_4:10:52:15531:4426:0:1:1 31 -
chr1 816310 816346 ILLUMINA-EAS45_4:10:43:6691:14007:0:1:1 31 -
chr1 816331 816367 ILLUMINA-EAS45_4:10:2:3789:6673:0:1:1 31 +
chr1 816769 816805 ILLUMINA-EAS45_4:10:17:2003:8825:0:1:1 31 -
chr1 817098 817134 ILLUMINA-EAS45_4:10:43:16259:2334:0:1:1 42 +
chr1 817137 817173 ILLUMINA-EAS45_4:10:103:7681:4852:0:1:1 31 +
chr1 817207 817243 ILLUMINA-EAS45_4:10:99:12147:14771:0:1:1 31 -